2144 lines
67 KiB
HTML
2144 lines
67 KiB
HTML
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<meta name="description" content="
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obimultiplex: demultiplex the sequence reads
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#
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Description
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#
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The
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obimultiplex
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command demultiplexes sequencing reads by identifying sample-specific tags (barcodes) and PCR primers in the sequences. It assigns each sequence to its corresponding sample based on the tag combinations and primer sequences provided in a sample description file.
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The demultiplexing process involves:
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Identifying forward and reverse PCR primers in the sequences.
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Detecting sample-specific tags.
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Assigning sequences to samples based on the tag/primer combinations.
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Trimming primers and tags from the sequences.
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Reverse complementing the sequences if needed.
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Adding comprehensive annotations about the identification process.
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The new obimultiplex sample description file format
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#
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If
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obimultiplex
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is still able to use the old ngsfilter format used by the legacy obitools, it is now preferable to rely on the new format.">
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<meta property="og:title" content="obimultiplex">
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<meta property="og:description" content="obimultiplex: demultiplex the sequence reads # Description # The obimultiplex command demultiplexes sequencing reads by identifying sample-specific tags (barcodes) and PCR primers in the sequences. It assigns each sequence to its corresponding sample based on the tag combinations and primer sequences provided in a sample description file.
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The demultiplexing process involves:
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Identifying forward and reverse PCR primers in the sequences. Detecting sample-specific tags. Assigning sequences to samples based on the tag/primer combinations. Trimming primers and tags from the sequences. Reverse complementing the sequences if needed. Adding comprehensive annotations about the identification process. The new obimultiplex sample description file format # If obimultiplex is still able to use the old ngsfilter format used by the legacy obitools, it is now preferable to rely on the new format.">
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<a href="/obidoc/docs/file_format/sequence_files/annotations/" class="">Annotation of sequences</a>
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<a href="/obidoc/formats/csv/" class="">The CSV format</a>
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<a href="/obidoc/obitools/obidistribute/" class="">obidistribute</a>
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<a href="/obidoc/obitools/obigrep/" class="">obigrep</a>
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<a href="/obidoc/obitools/obijoin/" class="">obijoin</a>
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<a href="/obidoc/obitools/obimatrix/" class="">obimatrix</a>
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<a href="/obidoc/obitools/obisplit/" class="">obisplit</a>
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<a href="/obidoc/obitools/obisummary/" class="">obisummary</a>
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<a href="/obidoc/obitools/obiuniq/" class="">obiuniq</a>
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<a role="button" class="">Demultiplexing samples</a>
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<a href="/obidoc/obitools/obimultiplex/" class="active">obimultiplex</a>
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<a href="/obidoc/obitools/obitagpcr/" class="">obitagpcr</a>
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<input type="checkbox" id="section-aa98fedd067b51150db59691a8ea8edd" class="toggle" />
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<label for="section-aa98fedd067b51150db59691a8ea8edd" class="flex justify-between">
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<a role="button" class="">Sequence alignments</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obiclean/" class="">obiclean</a>
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<ul>
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</ul>
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<input type="checkbox" id="section-7433746525d8c2b29b033f765c869acd" class="toggle" />
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<label for="section-7433746525d8c2b29b033f765c869acd" class="flex justify-between">
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<a href="/obidoc/obitools/obipairing/" class="">obipairing</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/docs/commands/alignments/obipairing/fasta-like/" class="">The FASTA-like alignment</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/docs/commands/alignments/obipairing/exact-alignment/" class="">Exact alignment</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obipcr/" class="">obipcr</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obirefidx/" class="">obirefidx</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obitag/" class="">obitag</a>
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<ul>
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</ul>
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</li>
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</ul>
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<input type="checkbox" id="section-5746f699d10490780dec8e30ab2dd3ce" class="toggle" />
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<label for="section-5746f699d10490780dec8e30ab2dd3ce" class="flex justify-between">
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<a role="button" class="">Taxonomy</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obitaxonomy/" class="">obitaxonomy</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-3f50c4fe7ab436a56ae92897d5444956" class="toggle" />
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<label for="section-3f50c4fe7ab436a56ae92897d5444956" class="flex justify-between">
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<a role="button" class="">Advanced tools</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obiscript/" class="">obiscript</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<label for="section-549be3934679fcb82a232f6bd5435563" class="flex justify-between">
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<a role="button" class="">Others</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obimicrosat/" class="">obimicrosat</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<input type="checkbox" id="section-ceca4455173761e30cbc0a6dc2327167" class="toggle" />
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<label for="section-ceca4455173761e30cbc0a6dc2327167" class="flex justify-between">
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<a role="button" class="">Experimentals</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obicleandb/" class="">obicleandb</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obiconsensus/" class="">obiconsensus</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obilandmark/" class="">obilandmark</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/commands/tags/" class="">Glossary of tags</a>
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</li>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-9b1bcd52530c59dc4819b1f61c128f54" class="toggle" />
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<label for="section-9b1bcd52530c59dc4819b1f61c128f54" class="flex justify-between">
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<a role="button" class="">Cookbook</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/docs/cookbook/illumina/" class="">Analysing an Illumina data set</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/cookbook/ecoprimers/" class="">Designing new barcodes</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/cookbook/local_genbank/" class="">Prepare a local copy of Genbank</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/cookbook/reference_db/" class="">Build a reference database</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/cookbook/minion/" class="">Oxford Nanopore data analysis</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<span>Programming OBITools</span>
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<ul>
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<li>
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<a href="/obidoc/docs/programming/expression/" class="">Expression language</a>
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<ul>
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</ul>
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</li>
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<li>
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<input type="checkbox" id="section-6d580829a667b5cca790b286d99a10fe" class="toggle" />
|
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<label for="section-6d580829a667b5cca790b286d99a10fe" class="flex justify-between">
|
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<a href="/obidoc/docs/programming/lua/" class="">Lua: for scripting OBITools</a>
|
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</label>
|
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<ul>
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<li>
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<input type="checkbox" id="section-2fb081dac812d624eea5f4268fca9e26" class="toggle" />
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<label for="section-2fb081dac812d624eea5f4268fca9e26" class="flex justify-between">
|
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<a role="button" class="">Obitools Classes</a>
|
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</label>
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<ul>
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<li>
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<a href="/obidoc/docs/programming/lua/obitools_classes/biosequence/" class="">BioSequence</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/programming/lua/obitools_classes/biosequenceslice/" class="">BioSequenceSlice</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/programming/lua/obitools_classes/taxonomy/" class="">Taxonomy</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/programming/lua/obitools_classes/taxon/" class="">Taxon</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/programming/lua/obitools_classes/mutex/" class="">Mutex</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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</nav>
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<script>(function(){var e=document.querySelector("aside .book-menu-content");addEventListener("beforeunload",function(){localStorage.setItem("menu.scrollTop",e.scrollTop)}),e.scrollTop=localStorage.getItem("menu.scrollTop")})()</script>
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</div>
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</aside>
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<div class="book-page">
|
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<header class="book-header">
|
|
|
|
<div class="flex align-center justify-between">
|
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<label for="menu-control">
|
|
<img src="/obidoc/svg/menu.svg" class="book-icon" alt="Menu" />
|
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</label>
|
|
|
|
<h3>obimultiplex</h3>
|
|
|
|
<label for="toc-control">
|
|
|
|
<img src="/obidoc/svg/toc.svg" class="book-icon" alt="Table of Contents" />
|
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|
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</label>
|
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</div>
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<aside class="hidden clearfix">
|
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|
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<nav id="TableOfContents">
|
|
<ul>
|
|
<li><a href="#obimultiplex-demultiplex-the-sequence-reads"><code>obimultiplex</code>: demultiplex the sequence reads</a>
|
|
<ul>
|
|
<li><a href="#description">Description</a>
|
|
<ul>
|
|
<li><a href="#the-new-obimultiplex-sample-description-file-format">The new <code>obimultiplex</code> sample description file format</a></li>
|
|
</ul>
|
|
</li>
|
|
<li><a href="#synopsis">Synopsis</a></li>
|
|
<li><a href="#options">Options</a>
|
|
<ul>
|
|
<li></li>
|
|
</ul>
|
|
</li>
|
|
<li><a href="#examples">Examples</a></li>
|
|
</ul>
|
|
</li>
|
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</ul>
|
|
</nav>
|
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</aside>
|
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</header>
|
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|
<article class="markdown book-article"><h1 id="obimultiplex-demultiplex-the-sequence-reads">
|
|
<code>obimultiplex</code>: demultiplex the sequence reads
|
|
<a class="anchor" href="#obimultiplex-demultiplex-the-sequence-reads">#</a>
|
|
</h1>
|
|
<h2 id="description">
|
|
Description
|
|
<a class="anchor" href="#description">#</a>
|
|
</h2>
|
|
<p>The <a href="http://metabar:8888/obidoc/obitools/obimultiplex/">
|
|
<abbr title="obimultiplex: "><code>obimultiplex</code></abbr>
|
|
</a> command demultiplexes sequencing reads by identifying sample-specific tags (barcodes) and PCR primers in the sequences. It assigns each sequence to its corresponding sample based on the tag combinations and primer sequences provided in a sample description file.</p>
|
|
<p>The demultiplexing process involves:</p>
|
|
<ul>
|
|
<li>Identifying forward and reverse PCR primers in the sequences.</li>
|
|
<li>Detecting sample-specific tags.</li>
|
|
<li>Assigning sequences to samples based on the tag/primer combinations.</li>
|
|
<li>Trimming primers and tags from the sequences.</li>
|
|
<li>Reverse complementing the sequences if needed.</li>
|
|
<li>Adding comprehensive annotations about the identification process.</li>
|
|
</ul>
|
|
<h3 id="the-new-obimultiplex-sample-description-file-format">
|
|
The new <code>obimultiplex</code> sample description file format
|
|
<a class="anchor" href="#the-new-obimultiplex-sample-description-file-format">#</a>
|
|
</h3>
|
|
<p>If <a href="http://metabar:8888/obidoc/obitools/obimultiplex/">
|
|
<abbr title="obimultiplex: "><code>obimultiplex</code></abbr>
|
|
</a> is still able to use the old <em>ngsfilter</em> format used by the legacy obitools, it is now preferable to rely on the new format.</p>
|
|
<p>The new format is a
|
|
<a href="http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/">CSV</a>
|
|
file, which can easily be prepared using an export from your favourite spreadsheet program.</p>
|
|
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-csv" data-lang="csv"><span style="display:flex;"><span><span style="color:#e6db74"># primer matching options</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">@param</span>,<span style="color:#e6db74">primer_mismatches</span>,<span style="color:#e6db74">2</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">@param</span>,<span style="color:#e6db74">indels</span>,<span style="color:#e6db74">false</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74"># tag matching options</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">@param</span>,<span style="color:#e6db74">matching</span>,<span style="color:#e6db74">strict</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">experiment</span>,<span style="color:#e6db74">sample</span>,<span style="color:#e6db74">sample_tag</span>,<span style="color:#e6db74">forward_primer</span>,<span style="color:#e6db74">reverse_primer</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">wolf_diet</span>,<span style="color:#e6db74">13a_F730603</span>,<span style="color:#e6db74">aattaac</span>,<span style="color:#e6db74">TTAGATACCCCACTATGC</span>,<span style="color:#e6db74">TAGAACAGGCTCCTCTAG</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">wolf_diet</span>,<span style="color:#e6db74">15a_F730814</span>,<span style="color:#e6db74">gaagtag</span>,<span style="color:#e6db74">TTAGATACCCCACTATGC</span>,<span style="color:#e6db74">TAGAACAGGCTCCTCTAG</span>
|
|
</span></span></code></pre></div><p>The
|
|
<a href="http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/">CSV</a>
|
|
file is divided into two sections. The first section consists of lines beginning with <code>@param</code> in the first cell. These lines specify the parameters used to match the primers and tags to the sequence. The second section provides a description of all the samples (PCRs) included in the sequencing library. This section begins with a line containing the names of the columns used to describe the samples in the subsequent lines. Only the second section is required.</p>
|
|
<h4 id="basic-format-and-required-columns">
|
|
Basic format and required columns
|
|
<a class="anchor" href="#basic-format-and-required-columns">#</a>
|
|
</h4>
|
|
<p>Below is an example for the minimal description of the PCRs multiplexed in the
|
|
sequencing library. In the new version of <em>OBITools4</em> this file is a
|
|
<a href="http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/">CSV</a>
|
|
file.</p>
|
|
<p>The first line is mandatory and must contains at least the five column names presented below:</p>
|
|
<ul>
|
|
<li>
|
|
<p><code>experiment</code>: the name of the experiment that allows for grouping of samples;</p>
|
|
</li>
|
|
<li>
|
|
<p><code>sample</code>: the sample (PCR) name;</p>
|
|
</li>
|
|
<li>
|
|
<p><code>sample_tag</code>: the tag identifying the sample:</p>
|
|
<p>Each sample tag must be unique within the library for each pair of primers. They can be
|
|
provided in upper or lower case. No distinction is made between the two.</p>
|
|
<ul>
|
|
<li>
|
|
<p>They can be a simple DNA word as here. This means that the same tag is used
|
|
for both forward and reverse primers (eg: <code>aattaac</code>).</p>
|
|
</li>
|
|
<li>
|
|
<p>It can be two DNA words separated by a colon. For example, <code>aagtag:gaagtag</code>.
|
|
This means that the first tag is used for the forward primer and the second for the
|
|
reverse primers.</p>
|
|
|
|
<link rel="stylesheet" href="/obidoc/css/vendors/admonitions.5c73bad2903e7d2d44ad118370ebd8c2cf5f239d4d93c283e55c00f2f8d30746.css" integrity="sha256-XHO60pA+fS1ErRGDcOvYws9fI51Nk8KD5VwA8vjTB0Y=" crossorigin="anonymous">
|
|
<div class="admonition note">
|
|
<div class="admonition-header"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 576 512"><path d="M0 64C0 28.7 28.7 0 64 0L224 0l0 128c0 17.7 14.3 32 32 32l128 0 0 125.7-86.8 86.8c-10.3 10.3-17.5 23.1-21 37.2l-18.7 74.9c-2.3 9.2-1.8 18.8 1.3 27.5L64 512c-35.3 0-64-28.7-64-64L0 64zm384 64l-128 0L256 0 384 128zM549.8 235.7l14.4 14.4c15.6 15.6 15.6 40.9 0 56.6l-29.4 29.4-71-71 29.4-29.4c15.6-15.6 40.9-15.6 56.6 0zM311.9 417L441.1 287.8l71 71L382.9 487.9c-4.1 4.1-9.2 7-14.9 8.4l-60.1 15c-5.5 1.4-11.2-.2-15.2-4.2s-5.6-9.7-4.2-15.2l15-60.1c1.4-5.6 4.3-10.8 8.4-14.9z"/></svg>
|
|
<span>The example presented above :<code>aattaac</code> is equivalent to <code>aattaac:aattaac</code>.</span>
|
|
</div>
|
|
</div></li>
|
|
<li>
|
|
<p>In the two-word syntax, if a forward or reverse primer is not tagged, the tag
|
|
is replaced by a hyphen. For example, <code>aagtag:-</code> or <code>-:aagtag</code>. Consequently, an
|
|
experiments conducted without primer tags must declare a dummy tag: <code>-:-</code>.</p>
|
|
</li>
|
|
</ul>
|
|
|
|
<div class="admonition caution">
|
|
<div class="admonition-header"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path d="M256 32c14.2 0 27.3 7.5 34.5 19.8l216 368c7.3 12.4 7.3 27.7 .2 40.1S486.3 480 472 480L40 480c-14.3 0-27.6-7.7-34.7-20.1s-7-27.8 .2-40.1l216-368C228.7 39.5 241.8 32 256 32zm0 128c-13.3 0-24 10.7-24 24l0 112c0 13.3 10.7 24 24 24s24-10.7 24-24l0-112c0-13.3-10.7-24-24-24zm32 224a32 32 0 1 0 -64 0 32 32 0 1 0 64 0z"/></svg>
|
|
<span>For a given primer all the tags must have the same length.</span>
|
|
</div>
|
|
</div></li>
|
|
<li>
|
|
<p>forward_primer: the forward primer sequence</p>
|
|
</li>
|
|
<li>
|
|
<p>reverse_primer: the reverse primer sequence</p>
|
|
</li>
|
|
</ul>
|
|
|
|
<a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
|
|
href="samples_simple.csv" download="samples_simple.csv">📄 samples_simple.csv</a>
|
|
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
|
|
|
|
<div class="highlight"><div style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;">
|
|
<table style="border-spacing:0;padding:0;margin:0;border:0;"><tr><td style="vertical-align:top;padding:0;margin:0;border:0;">
|
|
<pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">1
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">2
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">3
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">4
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">5
|
|
</span></code></pre></td>
|
|
<td style="vertical-align:top;padding:0;margin:0;border:0;;width:100%">
|
|
<pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-csv" data-lang="csv"><span style="display:flex;"><span><span style="color:#e6db74">experiment</span>,<span style="color:#e6db74">sample</span>,<span style="color:#e6db74">sample_tag</span>,<span style="color:#e6db74">forward_primer</span>,<span style="color:#e6db74">reverse_primer</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">wolf_diet</span>,<span style="color:#e6db74">13a_F730603</span>,<span style="color:#e6db74">aattaac</span>,<span style="color:#e6db74">TTAGATACCCCACTATGC</span>,<span style="color:#e6db74">TAGAACAGGCTCCTCTAG</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">wolf_diet</span>,<span style="color:#e6db74">15a_F730814</span>,<span style="color:#e6db74">gaagtag</span>,<span style="color:#e6db74">TTAGATACCCCACTATGC</span>,<span style="color:#e6db74">TAGAACAGGCTCCTCTAG</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">wolf_diet</span>,<span style="color:#e6db74">26a_F040644</span>,<span style="color:#e6db74">gaatatc</span>,<span style="color:#e6db74">TTAGATACCCCACTATGC</span>,<span style="color:#e6db74">TAGAACAGGCTCCTCTAG</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">wolf_diet</span>,<span style="color:#e6db74">29a_F260619</span>,<span style="color:#e6db74">gcctcct</span>,<span style="color:#e6db74">TTAGATACCCCACTATGC</span>,<span style="color:#e6db74">TAGAACAGGCTCCTCTAG</span>
|
|
</span></span></code></pre></td></tr></table>
|
|
</div>
|
|
</div></td>
|
|
|
|
</DIV>
|
|
|
|
|
|
<a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
|
|
href="wolf_4seq.fastq" download="wolf_4seq.fastq">📄 wolf_4seq.fastq</a>
|
|
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
|
|
|
|
<pre tabindex="0"><code class="language-fastq" data-lang="fastq">@HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/1
|
|
ccaattaactagaacaggctcgtctagaagggtataaagcaccgccaagtcctttgagttttaagctattgccggtagtactctggcgaatagttttgtttgcataactatttgtgtttaaggctaggcatagtggggtatctaagttaattgg
|
|
+
|
|
CCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCC=CBCCBCBCCCCCCDEFAEDEEEEBEAEJEJ?D?CD@^aVca\C????CEBC>I?D<>EEDDDEEEEEEEAFEEDECCCCCCCCCCCCCCCBCCCCCCBCCCCCCCCCDCCCCCCCCCCCBC
|
|
@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/1
|
|
ccgaatatcttagataccccactatgcttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccctctagaggagcctgttctagatattcgg
|
|
+
|
|
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCacZXceafbd_e_bVb`cb[WZb]aaaaV`ECDDCEDCDKECFFEEEEEDEDEEJEEE@EEJECCCCCBCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCBCC
|
|
@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1
|
|
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
|
|
+
|
|
CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
|
|
@HELIUM_000100422_612GNAAXX:7:108:6440:4223#0/1
|
|
ccgcctcctttagatcccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
|
|
+
|
|
CCCCCCCBCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
|
|
</code></pre></td>
|
|
|
|
</DIV>
|
|
|
|
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obimultiplex -s samples_simple.csv <span style="color:#ae81ff">\
|
|
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> wolf_4seq.fastq <span style="color:#ae81ff">\
|
|
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> > wolf_4seq_simple.fastq
|
|
</span></span></code></pre></div>
|
|
<a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
|
|
href="wolf_4seq_simple.fastq" download="wolf_4seq_simple.fastq">📄 wolf_4seq_simple.fastq</a>
|
|
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
|
|
|
|
<pre tabindex="0"><code class="language-fastq" data-lang="fastq">@HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/1_sub[28..127] {"experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"reverse","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"aattaac","obimultiplex_forward_tag":"aattaac","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":1,"obimultiplex_reverse_match":"tagaacaggctcgtctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"aattaac","obimultiplex_reverse_tag":"aattaac","obimultiplex_reverse_tag_dist":0,"sample":"13a_F730603"}
|
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
|
+
|
|
CCCBCCCCCCCCCCCCCCCEDEEFAEEEEEEEDDDEE><D?I>CBEC????C\acVa^@DC?D?JEJEAEBEEEEDEAFEDCCCCCCBCBCCBC=CCCCC
|
|
@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/1_sub[28..126] {"experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"forward","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"gaatatc","obimultiplex_forward_tag":"gaatatc","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":0,"obimultiplex_reverse_match":"tagaacaggctcctctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"gaatatc","obimultiplex_reverse_tag":"gaatatc","obimultiplex_reverse_tag_dist":0,"sample":"26a_F040644"}
|
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
|
|
+
|
|
CCCCCCCCCCCCCCCCCCacZXceafbd_e_bVb`cb[WZb]aaaaV`ECDDCEDCDKECFFEEEEEDEDEEJEEE@EEJECCCCCBCCCCCCCCCCCC
|
|
@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1_sub[28..127] {"experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"forward","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"gcctcct","obimultiplex_forward_tag":"gcctcct","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":0,"obimultiplex_reverse_match":"tagaacaggctcctctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"gcctcct","obimultiplex_reverse_tag":"gcctcct","obimultiplex_reverse_tag_dist":0,"sample":"29a_F260619"}
|
|
ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
|
+
|
|
CCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCC
|
|
</code></pre></td>
|
|
|
|
</DIV>
|
|
|
|
<ul>
|
|
<li>
|
|
<p>Sample description</p>
|
|
<ul>
|
|
<li>
|
|
<p><code>experiment</code>: “wolf_diet”</p>
|
|
<p>The experiment name imputed to the barcode sequence</p>
|
|
</li>
|
|
<li>
|
|
<p><code>sample</code>: “13a_F730603”</p>
|
|
<p>The sample (PCR) name imputed to the barcode sequence</p>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<p>Amplicon description</p>
|
|
<ul>
|
|
<li>
|
|
<p><code>obimultiplex_amplicon_rank</code>: “1/1”</p>
|
|
<a href="http://metabar:8888/obidoc/obitools/obimultiplex/">
|
|
<abbr title="obimultiplex: "><code>obimultiplex</code></abbr>
|
|
</a> is able to detect concatemer of several amplicons. This information
|
|
is reported in the `obimultiplex_amplicon_rank` as a ratio here "1/1" meaning the first among one in the read. A value of "2/3" would mean the second amplicon detected among three in the read.
|
|
</li>
|
|
<li>
|
|
<p><code>obimultiplex_direction</code>: “reverse”</p>
|
|
<p>The direction in which the amplicon has been detected:</p>
|
|
<ul>
|
|
<li>
|
|
<p>“forward” means, the forward primer has been identified, then the reverse complementary sequence of the reverse primer.</p>
|
|
</li>
|
|
<li>
|
|
<p>“reverse” means, the reverse primer has been identified, then the forward complementary sequence of the forward primer. The sequence of the barcode has been reverse complemented to be always reported as a sequence oriented from the forward to the reverse primer.</p>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<p>Primer matching</p>
|
|
<ul>
|
|
<li>
|
|
<p>Forward primer:</p>
|
|
<ul>
|
|
<li>
|
|
<p><code>obimultiplex_forward_primer</code>: “ttagataccccactatgc”</p>
|
|
<p>The true forward primer sequence as provided in the <a href="http://metabar:8888/obidoc/obitools/obimultiplex/">
|
|
<abbr title="obimultiplex: "><code>obimultiplex</code></abbr>
|
|
</a> sample description file.</p>
|
|
</li>
|
|
<li>
|
|
<p><code>obimultiplex_forward_match</code>: “ttagataccccactatgc”</p>
|
|
<p>The primer sequence as detected in the sequence read.</p>
|
|
</li>
|
|
<li>
|
|
<p><code>obimultiplex_forward_error</code>: 0</p>
|
|
<p>The number of differences between the <code>obimultiplex_forward_primer</code> and the <code>obimultiplex_forward_match</code> attribute values. <a href="http://metabar:8888/obidoc/obitools/obimultiplex/">
|
|
<abbr title="obimultiplex: "><code>obimultiplex</code></abbr>
|
|
</a> by default
|
|
allows up to two mismatches. That threshold can be changed using the <strong>–allowed-mismatches</strong> option (or <strong>-e</strong> for the short version option).</p>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<p>Reverse primer:</p>
|
|
<ul>
|
|
<li>
|
|
<p>“obimultiplex_reverse_primer”:“tagaacaggctcctctag”</p>
|
|
<p>The true reverse primer sequence as provided in the <a href="http://metabar:8888/obidoc/obitools/obimultiplex/">
|
|
<abbr title="obimultiplex: "><code>obimultiplex</code></abbr>
|
|
</a> sample description file.</p>
|
|
</li>
|
|
<li>
|
|
<p>“obimultiplex_reverse_match”:“tagaacaggctcgtctag”</p>
|
|
<p>The primer sequence as detected in the sequence read.</p>
|
|
</li>
|
|
<li>
|
|
<p>“obimultiplex_reverse_error”:1</p>
|
|
<p>Here one mismatch has been detected between the primer sequence and the read sequence match.</p>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<p>Tag identification</p>
|
|
<ul>
|
|
<li>Forward tag:
|
|
<ul>
|
|
<li>“obimultiplex_forward_tag”:“gcctcct”</li>
|
|
<li>“obimultiplex_forward_proposed_tag”:“gcctcct”</li>
|
|
<li>“obimultiplex_forward_matching”:“strict”</li>
|
|
<li>“obimultiplex_forward_tag_dist”:0</li>
|
|
</ul>
|
|
</li>
|
|
<li>Reverse tag:
|
|
<ul>
|
|
<li>“obimultiplex_reverse_tag”:“gcctcct”</li>
|
|
<li>“obimultiplex_reverse_proposed_tag”:“gcctcct”</li>
|
|
<li>“obimultiplex_reverse_matching”:“strict”</li>
|
|
<li>“obimultiplex_reverse_tag_dist”:0</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h4 id="supplementary-columns">
|
|
Supplementary columns
|
|
<a class="anchor" href="#supplementary-columns">#</a>
|
|
</h4>
|
|
|
|
<a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
|
|
href="samples_extra.csv" download="samples_extra.csv">📄 samples_extra.csv</a>
|
|
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
|
|
|
|
<div class="highlight"><div style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;">
|
|
<table style="border-spacing:0;padding:0;margin:0;border:0;"><tr><td style="vertical-align:top;padding:0;margin:0;border:0;">
|
|
<pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">1
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">2
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">3
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">4
|
|
</span><span style="white-space:pre;-webkit-user-select:none;user-select:none;margin-right:0.4em;padding:0 0.4em 0 0.4em;color:#7f7f7f">5
|
|
</span></code></pre></td>
|
|
<td style="vertical-align:top;padding:0;margin:0;border:0;;width:100%">
|
|
<pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-csv" data-lang="csv"><span style="display:flex;"><span><span style="color:#e6db74">experiment</span>,<span style="color:#e6db74">sample</span>,<span style="color:#e6db74">sample_tag</span>,<span style="color:#e6db74">forward_primer</span>,<span style="color:#e6db74">reverse_primer</span>,<span style="color:#e6db74">sex</span>,<span style="color:#e6db74">age</span>,<span style="color:#e6db74">plate</span>,<span style="color:#e6db74">position</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">wolf_diet</span>,<span style="color:#e6db74">13a_F730603</span>,<span style="color:#e6db74">aattaac</span>,<span style="color:#e6db74">TTAGATACCCCACTATGC</span>,<span style="color:#e6db74">TAGAACAGGCTCCTCTAG</span>,<span style="color:#e6db74">male</span>,<span style="color:#e6db74">adult</span>,<span style="color:#e6db74">02</span>,<span style="color:#e6db74">A03</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">wolf_diet</span>,<span style="color:#e6db74">15a_F730814</span>,<span style="color:#e6db74">gaagtag</span>,<span style="color:#e6db74">TTAGATACCCCACTATGC</span>,<span style="color:#e6db74">TAGAACAGGCTCCTCTAG</span>,<span style="color:#e6db74">male</span>,<span style="color:#e6db74">juvenile</span>,<span style="color:#e6db74">02</span>,<span style="color:#e6db74">A01</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">wolf_diet</span>,<span style="color:#e6db74">26a_F040644</span>,<span style="color:#e6db74">gaatatc</span>,<span style="color:#e6db74">TTAGATACCCCACTATGC</span>,<span style="color:#e6db74">TAGAACAGGCTCCTCTAG</span>,<span style="color:#e6db74">female</span>,<span style="color:#e6db74">adult</span>,<span style="color:#e6db74">01</span>,<span style="color:#e6db74">B08</span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#e6db74">wolf_diet</span>,<span style="color:#e6db74">29a_F260619</span>,<span style="color:#e6db74">gcctcct</span>,<span style="color:#e6db74">TTAGATACCCCACTATGC</span>,<span style="color:#e6db74">TAGAACAGGCTCCTCTAG</span>,<span style="color:#e6db74">female</span>,<span style="color:#e6db74">adult</span>,<span style="color:#e6db74">01</span>,<span style="color:#e6db74">B12</span>
|
|
</span></span></code></pre></td></tr></table>
|
|
</div>
|
|
</div></td>
|
|
|
|
</DIV>
|
|
|
|
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obimultiplex -s samples_extra.csv <span style="color:#ae81ff">\
|
|
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> wolf_4seq.fastq <span style="color:#ae81ff">\
|
|
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> > wolf_4seq_extra.fastq
|
|
</span></span></code></pre></div>
|
|
<a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
|
|
href="wolf_4seq_extra.fastq" download="wolf_4seq_extra.fastq">📄 wolf_4seq_extra.fastq</a>
|
|
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
|
|
|
|
<pre tabindex="0"><code class="language-fastq" data-lang="fastq">@HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/1_sub[28..127] {"age":"adult","experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"reverse","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"aattaac","obimultiplex_forward_tag":"aattaac","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":1,"obimultiplex_reverse_match":"tagaacaggctcgtctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"aattaac","obimultiplex_reverse_tag":"aattaac","obimultiplex_reverse_tag_dist":0,"plate":"02","position":"A03","sample":"13a_F730603","sex":"male"}
|
|
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
|
+
|
|
CCCBCCCCCCCCCCCCCCCEDEEFAEEEEEEEDDDEE><D?I>CBEC????C\acVa^@DC?D?JEJEAEBEEEEDEAFEDCCCCCCBCBCCBC=CCCCC
|
|
@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/1_sub[28..126] {"age":"adult","experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"forward","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"gaatatc","obimultiplex_forward_tag":"gaatatc","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":0,"obimultiplex_reverse_match":"tagaacaggctcctctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"gaatatc","obimultiplex_reverse_tag":"gaatatc","obimultiplex_reverse_tag_dist":0,"plate":"01","position":"B08","sample":"26a_F040644","sex":"female"}
|
|
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
|
|
+
|
|
CCCCCCCCCCCCCCCCCCacZXceafbd_e_bVb`cb[WZb]aaaaV`ECDDCEDCDKECFFEEEEEDEDEEJEEE@EEJECCCCCBCCCCCCCCCCCC
|
|
@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1_sub[28..127] {"age":"adult","experiment":"wolf_diet","obimultiplex_amplicon_rank":"1/1","obimultiplex_direction":"forward","obimultiplex_forward_error":0,"obimultiplex_forward_match":"ttagataccccactatgc","obimultiplex_forward_matching":"strict","obimultiplex_forward_primer":"ttagataccccactatgc","obimultiplex_forward_proposed_tag":"gcctcct","obimultiplex_forward_tag":"gcctcct","obimultiplex_forward_tag_dist":0,"obimultiplex_reverse_error":0,"obimultiplex_reverse_match":"tagaacaggctcctctag","obimultiplex_reverse_matching":"strict","obimultiplex_reverse_primer":"tagaacaggctcctctag","obimultiplex_reverse_proposed_tag":"gcctcct","obimultiplex_reverse_tag":"gcctcct","obimultiplex_reverse_tag_dist":0,"plate":"01","position":"B12","sample":"29a_F260619","sex":"female"}
|
|
ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
|
+
|
|
CCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCC
|
|
</code></pre></td>
|
|
|
|
</DIV>
|
|
|
|
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obimultiplex -s samples_simple.csv <span style="color:#ae81ff">\
|
|
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> -u wolf_4seq_bad.fastq <span style="color:#ae81ff">\
|
|
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> wolf_4seq.fastq <span style="color:#ae81ff">\
|
|
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> > wolf_4seq_simple.fastq
|
|
</span></span></code></pre></div>
|
|
<a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
|
|
href="wolf_4seq_bad.fastq" download="wolf_4seq_bad.fastq">📄 wolf_4seq_bad.fastq</a>
|
|
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
|
|
|
|
<pre tabindex="0"><code class="language-fastq" data-lang="fastq">@HELIUM_000100422_612GNAAXX:7:108:6440:4223#0/1 {"obimultiplex_error":"No barcode identified"}
|
|
ccgcctcctttagatcccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
|
|
+
|
|
CCCCCCCBCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
|
|
</code></pre></td>
|
|
|
|
</DIV>
|
|
|
|
<h2 id="synopsis">
|
|
Synopsis
|
|
<a class="anchor" href="#synopsis">#</a>
|
|
</h2>
|
|
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obimultiplex <span style="color:#f92672">[</span>--allowed-mismatches|-e <int><span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--batch-size <int><span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--compress|-Z<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--debug<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--ecopcr<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--embl<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--fasta<span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--fasta-output<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--fastq<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--fastq-output<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--force-one-cpu<span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--genbank<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--help|-h|-?<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--input-OBI-header<span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--input-json-header<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--json-output<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--keep-errors<span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--max-cpu <int><span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--no-order<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--no-progressbar<span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--out|-o <FILENAME><span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--output-OBI-header|-O<span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--output-json-header<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--paired-with <FILENAME><span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--pprof<span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--pprof-goroutine <int><span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--pprof-mutex <int><span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--skip-empty<span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--solexa<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--tag-list|-s <string><span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--taxonomy|-t <string><span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--template<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--unidentified|-u <string><span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--version<span style="color:#f92672">]</span>
|
|
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--with-indels<span style="color:#f92672">]</span> <span style="color:#f92672">[</span><args><span style="color:#f92672">]</span>
|
|
</span></span></code></pre></div><h2 id="options">
|
|
Options
|
|
<a class="anchor" href="#options">#</a>
|
|
</h2>
|
|
<h4 id="hahahugoshortcode31s16hbhb-specific-options">
|
|
<a href="http://metabar:8888/obidoc/obitools/obimultiplex/">
|
|
<abbr title="obimultiplex: "><code>obimultiplex</code></abbr>
|
|
</a> specific options
|
|
<a class="anchor" href="#hahahugoshortcode31s16hbhb-specific-options">#</a>
|
|
</h4>
|
|
<ul>
|
|
<li><b><code class="language-bash">--allowed-mismatches</code></b>
|
|
| <b><code class="language-bash">-e</code></b>
|
|
<INTEGER>: Used to specify the number of errors allowed for matching primers. (default: -1)</li>
|
|
<li><b><code class="language-bash">--keep-errors</code></b>: Prints symbol counts. (default: false)</li>
|
|
<li><b><code class="language-bash">--paired-with</code></b> <FILENAME>: filename containing the paired reads.</li>
|
|
<li><b><code class="language-bash">--tag-list</code></b>
|
|
| <b><code class="language-bash">-s</code></b>
|
|
<string>: File name of the NGSFilter file describing PCRs.</li>
|
|
<li><b><code class="language-bash">--template</code></b>: Print on the standard output an example of CSV configuration file. (default: false)
|
|
</li>
|
|
<li><b><code class="language-bash">--unidentified</code></b>
|
|
| <b><code class="language-bash">-u</code></b>
|
|
<string>: Filename used to store the sequences unassigned to any sample.
|
|
</li>
|
|
<li><b><code class="language-bash">--with-indels</code></b>: Allows for indels during the primers matching. (default: false)
|
|
</li>
|
|
</ul>
|
|
<h4 id="taxonomic-options">
|
|
Taxonomic options
|
|
<a class="anchor" href="#taxonomic-options">#</a>
|
|
</h4>
|
|
<ul>
|
|
<li><b><code class="language-bash">--taxonomy</code></b>
|
|
| <b><code class="language-bash">-t</code></b>
|
|
<string>: Path to the taxonomic database.
|
|
</li>
|
|
</ul>
|
|
<h4 id="controlling-the-input-data">
|
|
Controlling the input data
|
|
<a class="anchor" href="#controlling-the-input-data">#</a>
|
|
</h4>
|
|
|
|
|
|
<I>OBITools4</I> generally recognizes the input file format. It also recognizes
|
|
whether the input file is compressed using GZIP. But some rare files can be
|
|
misidentified, so the following options allow the user to force the format, thus
|
|
bypassing the format identification step.
|
|
|
|
<h5 id="the-file-format-options">
|
|
The file format options
|
|
<a class="anchor" href="#the-file-format-options">#</a>
|
|
</h5>
|
|
|
|
|
|
<ul>
|
|
<li>
|
|
<b><code class="language-bash">--fasta</code></b>: indicates that sequence data is in <a href="http://metabar:8888/obidoc/formats/fasta/">fasta</a> format.</li>
|
|
<li>
|
|
<b><code class="language-bash">--fastq</code></b>: indicates that sequence data is in <a href="http://metabar:8888/obidoc/formats/fastq/">fastq</a> format.</li>
|
|
<li>
|
|
<b><code class="language-bash">--embl</code></b>: indicates that sequence data is in <a href="http://metabar:8888/obidoc/formats/embl/">EMBL-ENA flatfile</a> format.</li>
|
|
<li>
|
|
<b><code class="language-bash">--csv</code></b>: indicates that sequence data is in <a href="http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/">CSV</a> format.</li>
|
|
<li>
|
|
<b><code class="language-bash">--genbank</code></b>: indicates that sequence data is in <a href="http://metabar:8888/obidoc/formats/genbank/">GenBank flatfile</a> format.</li>
|
|
<li><b><code class="language-bash">--ecopcr</code></b>: indicates that sequence data is in the old ecoPCR tabulated format.</li>
|
|
</ul>
|
|
|
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<h5 id="controlling-the-way-obitools4-are-formatting-annotations">
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Controlling the way <em>OBITools4</em> are formatting annotations
|
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<a class="anchor" href="#controlling-the-way-obitools4-are-formatting-annotations">#</a>
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</h5>
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These options only apply to the <a href="http://metabar:8888/obidoc/formats/fasta/">FASTA</a> and <a href="http://metabar:8888/obidoc/formats/fastq/">FASTQ</a> formats
|
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<ul>
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<li><b><code class="language-bash">--input-OBI-header</code></b>: FASTA/FASTQ title line annotations follow the old OBI format.</li>
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<li><b><code class="language-bash">--input-json-header</code></b>: FASTA/FASTQ title line annotations follow the JSON format.</li>
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</ul>
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<h5 id="controlling-quality-score-decoding">
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Controlling quality score decoding
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|
<a class="anchor" href="#controlling-quality-score-decoding">#</a>
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</h5>
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This option only applies to the <a href="http://metabar:8888/obidoc/formats/fastq/">FASTQ</a> formats
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<ul>
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<li><b><code class="language-bash">--solexa</code></b>: decodes quality string according to the old Solexa specification. (default: the standard Sanger encoding is used, env: <strong>OBISSOLEXA</strong>)</li>
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</ul>
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<h4 id="controlling-the-output-data">
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Controlling the output data
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<a class="anchor" href="#controlling-the-output-data">#</a>
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</h4>
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<ul>
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<li><b><code class="language-bash">--compress</code></b>
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| <b><code class="language-bash">-Z</code></b>
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|
: output is compressed using gzip. (default: false)</li>
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|
<li><b><code class="language-bash">--no-order</code></b>: the <em>OBITools</em> ensure that the order between the input file and
|
|
the output file does not change. When multiple files are processed,
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|
they are processed one at a time.
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|
If the <strong>–no-order</strong> option is added to a command, multiple input
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|
files can be opened at the same time and their contents processed
|
|
in parallel. This usually increases processing speed, but does not
|
|
guarantee the order of the sequences in the output file.
|
|
Also, processing multiple files in parallel may require more memory
|
|
to perform the computation.</li>
|
|
<li>
|
|
<b><code class="language-bash">--fasta-output</code></b>: writes sequence data in <a href="http://metabar:8888/obidoc/formats/fasta/">fasta</a> format (default if quality data is not available).</li>
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|
<li>
|
|
<b><code class="language-bash">--fastq-output</code></b>: writes sequence data in <a href="http://metabar:8888/obidoc/formats/fastq/">fastq</a> format (default if quality data is available).</li>
|
|
<li><b><code class="language-bash">--json-output</code></b>: writes sequence data in JSON format.</li>
|
|
<li><b><code class="language-bash">--out</code></b>
|
|
| <b><code class="language-bash">-o</code></b>
|
|
<FILENAME>: filename used for saving the output (default: “-”, the standard output)</li>
|
|
<li><b><code class="language-bash">--output-OBI-header</code></b>
|
|
| <b><code class="language-bash">-O</code></b>
|
|
: writes output FASTA/FASTQ title line annotations in OBI format (default: JSON).</li>
|
|
<li><b><code class="language-bash">--output-json-header</code></b>: writew output FASTA/FASTQ title line annotations in JSON format (the default format).</li>
|
|
<li><b><code class="language-bash">--skip-empty</code></b>: sequences of length equal to zero are removed from the output (default: false).</li>
|
|
<li><b><code class="language-bash">--no-progressbar</code></b>: deactivates progress bar display (default: false).</li>
|
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</ul>
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|
<h4 id="general-options">
|
|
General options
|
|
<a class="anchor" href="#general-options">#</a>
|
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</h4>
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<ul>
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|
<li><b><code class="language-bash">--help</code></b>
|
|
| <b><code class="language-bash">-h|-?</code></b>
|
|
: shows this help.</li>
|
|
<li><b><code class="language-bash">--version</code></b>: prints the version and exits.</li>
|
|
<li><b><code class="language-bash">--silent-warning</code></b>: This option tells obitools to stop displaying warnings.
|
|
This behaviour can be controlled by setting the <strong>OBIWARNINGS</strong> environment variable.</li>
|
|
</ul>
|
|
|
|
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|
<h4 id="computation-related-options">
|
|
Computation related options
|
|
<a class="anchor" href="#computation-related-options">#</a>
|
|
</h4>
|
|
|
|
|
|
<ul>
|
|
<li><b><code class="language-bash">--max-cpu</code></b> <INTEGER>: <em>OBITools</em> can take advantage of your computer’s multi-core
|
|
architecture by parallelizing the computation across all available CPUs.
|
|
Computing on more CPUs usually requires more memory to perform the
|
|
computation. Reducing the number of CPUs used to perform a calculation
|
|
is also a way to indirectly control the amount of memory used by the
|
|
process. The number of CPUs used by <em>OBITools</em> can also be controlled
|
|
by setting the <strong>OBIMAXCPU</strong> environment variable.</li>
|
|
<li><b><code class="language-bash">--force-one-cpu</code></b>: forces the use of a single CPU core for parallel processing (default: false).</li>
|
|
<li><b><code class="language-bash">--batch-size</code></b> <INTEGER>: number of sequence per batch for parallel processing (default: 1000, env: <strong>OBIBATCHSIZE</strong>)</li>
|
|
</ul>
|
|
|
|
<h4 id="debug-related-options">
|
|
Debug related options
|
|
<a class="anchor" href="#debug-related-options">#</a>
|
|
</h4>
|
|
|
|
|
|
<ul>
|
|
<li><b><code class="language-bash">--debug</code></b>: enables debug mode, by setting log level to debug (default: false, env: <strong>OBIDEBUG</strong>)</li>
|
|
<li><b><code class="language-bash">--pprof</code></b>: enables pprof server. Look at the log for details. (default: false).</li>
|
|
<li><b><code class="language-bash">--pprof-mutex</code></b> <INTEGER>: enables profiling of mutex lock. (default: 10, env: <strong>OBIPPROFMUTEX</strong>)</li>
|
|
<li><b><code class="language-bash">--pprof-goroutine</code></b> <INTEGER>: enables profiling of goroutine blocking profile. (default: 6060, env: <strong>OBIPPROFGOROUTINE</strong>)</li>
|
|
</ul>
|
|
<h2 id="examples">
|
|
Examples
|
|
<a class="anchor" href="#examples">#</a>
|
|
</h2>
|
|
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obimultiplex --help
|
|
</span></span></code></pre></div></article>
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<div class="book-toc-content">
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<nav id="TableOfContents">
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<ul>
|
|
<li><a href="#obimultiplex-demultiplex-the-sequence-reads"><code>obimultiplex</code>: demultiplex the sequence reads</a>
|
|
<ul>
|
|
<li><a href="#description">Description</a>
|
|
<ul>
|
|
<li><a href="#the-new-obimultiplex-sample-description-file-format">The new <code>obimultiplex</code> sample description file format</a></li>
|
|
</ul>
|
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</li>
|
|
<li><a href="#synopsis">Synopsis</a></li>
|
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<li><a href="#options">Options</a>
|
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<ul>
|
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<li></li>
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</ul>
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</li>
|
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<li><a href="#examples">Examples</a></li>
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</li>
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