1590 lines
25 KiB
HTML
1590 lines
25 KiB
HTML
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<meta name="description" content="
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What are OBITools4?
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#
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The development of OBITools
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began at
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LECA
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(
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University of Grenoble) in the early 2000s, at the same time as the development of DNA metabarcoding methods in the same laboratory. The idea behind the OBITools project was to provide a set of UNIX command-line tools that mimic standard UNIX shell commands such as grep, uniq or wc, but which work on DNA sequence files. Unlike standard UNIX tools, where the processing unit is a line of text, with OBITools the processing unit is a sequence record. In addition, some commands implementing algorithms specific to the processing of DNA metabarcoding data have been added, making OBITools
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one of the sequence processing tools widely used on UNIX-like systems, suitable for the analysis of DNA metabarcoding data.">
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<meta property="og:description" content="What are OBITools4? # The development of OBITools began at LECA ( University of Grenoble) in the early 2000s, at the same time as the development of DNA metabarcoding methods in the same laboratory. The idea behind the OBITools project was to provide a set of UNIX command-line tools that mimic standard UNIX shell commands such as grep, uniq or wc, but which work on DNA sequence files. Unlike standard UNIX tools, where the processing unit is a line of text, with OBITools the processing unit is a sequence record. In addition, some commands implementing algorithms specific to the processing of DNA metabarcoding data have been added, making OBITools one of the sequence processing tools widely used on UNIX-like systems, suitable for the analysis of DNA metabarcoding data.">
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<a href="/obidoc/docs/installation/" class="">Installation</a>
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<a role="button" class="">Sequence file formats</a>
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<ul>
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<a href="/obidoc/formats/fasta/" class="">FASTA file format</a>
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<a href="/obidoc/formats/fastq/" class="">FASTQ file format</a>
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<a href="/obidoc/formats/genbank/" class="">GenBank Flat File format</a>
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<a href="/obidoc/formats/embl/" class="">EMBL Flat File format</a>
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<a href="/obidoc/docs/file_format/sequence_files/csv/" class="">CSV format</a>
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<a href="/obidoc/formats/json/" class="">JSON format</a>
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<a href="/obidoc/docs/file_format/sequence_files/annotations/" class="">Annotation of sequences</a>
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<a role="button" class="">Taxonomy file formats</a>
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<a href="/obidoc/docs/file_format/taxonomy_file/csv_taxdump/" class="">CSV formatted taxdump</a>
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<a href="/obidoc/docs/file_format/taxonomy_file/ncbi_taxdump/" class="">NCBI taxdump</a>
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<ul>
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</ul>
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<a href="/obidoc/formats/csv/" class="">The CSV format</a>
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<ul>
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</ul>
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<label for="section-70b1e6e5ec7f3ccab643155fa50659b6" class="flex justify-between">
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<a role="button" class="">Patterns</a>
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</label>
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<a href="/obidoc/docs/patterns/regular/" class="">Regular Expressions</a>
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<a href="/obidoc/docs/patterns/dnagrep/" class="">DNA Patterns</a>
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</ul>
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<input type="checkbox" id="section-8223f464911a1fe6c655972143684e93" class="toggle" />
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<label for="section-8223f464911a1fe6c655972143684e93" class="flex justify-between">
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<a role="button" class="">The OBITools4 commands</a>
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</label>
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<ul>
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<a href="/obidoc/docs/commands/options/" class="">Shared command options</a>
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<input type="checkbox" id="section-8921ea65523c266b128dd4263232b0fc" class="toggle" />
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<label for="section-8921ea65523c266b128dd4263232b0fc" class="flex justify-between">
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<a role="button" class="">Basics</a>
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</label>
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<li>
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<a href="/obidoc/obitools/obiannotate/" class="">obiannotate</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obicomplement/" class="">obicomplement</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obiconvert/" class="">obiconvert</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obicount/" class="">obicount</a>
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<ul>
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<a href="/obidoc/obitools/obicsv/" class="">obicsv</a>
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</ul>
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<a href="/obidoc/obitools/obidemerge/" class="">obidemerge</a>
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<ul>
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<li>
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<a href="/obidoc/obitools/obidistribute/" class="">obidistribute</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obigrep/" class="">obigrep</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obijoin/" class="">obijoin</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obimatrix/" class="">obimatrix</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obisplit/" class="">obisplit</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obisummary/" class="">obisummary</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obiuniq/" class="">obiuniq</a>
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<ul>
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</ul>
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</ul>
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<input type="checkbox" id="section-dbdf1bb5377572439394e60e08c30f50" class="toggle" />
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<label for="section-dbdf1bb5377572439394e60e08c30f50" class="flex justify-between">
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<a role="button" class="">Demultiplexing samples</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obimultiplex/" class="">obimultiplex</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/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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<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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<a href="/obidoc/docs/commands/alignments/obipairing/fasta-like/" class="">The FASTA-like alignment</a>
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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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<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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<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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<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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<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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<input type="checkbox" id="section-549be3934679fcb82a232f6bd5435563" class="toggle" />
|
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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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<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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<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" />
|
|
<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">
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<div class="flex align-center justify-between">
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<label for="menu-control">
|
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<img src="/obidoc/svg/menu.svg" class="book-icon" alt="Menu" />
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</label>
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|
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<h3>About</h3>
|
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|
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<label for="toc-control">
|
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|
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<img src="/obidoc/svg/toc.svg" class="book-icon" alt="Table of Contents" />
|
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</label>
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</div>
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<aside class="hidden clearfix">
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<nav id="TableOfContents">
|
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<ul>
|
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<li>
|
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<ul>
|
|
<li><a href="#what-are-obitools4">What are OBITools4?</a></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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</aside>
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</header>
|
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<article class="markdown book-article"><h2 id="what-are-obitools4">
|
|
What are OBITools4?
|
|
<a class="anchor" href="#what-are-obitools4">#</a>
|
|
</h2>
|
|
<p>The development of <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
|
|
began at
|
|
<a href="https://leca.osug.fr"><abbr title="LECA: Laboratoire d'écologie Alpine - Laboratory for Alpine Ecology">LECA</abbr>
|
|
|
|
</a> (
|
|
<a href="https://www.univ-grenoble-alpes.fr/">University of Grenoble</a>) in the early 2000s, at the same time as the development of DNA metabarcoding methods in the same laboratory. The idea behind the OBITools project was to provide a set of UNIX command-line tools that mimic standard UNIX shell commands such as <code>grep</code>, <code>uniq</code> or <code>wc</code>, but which work on DNA sequence files. Unlike standard UNIX tools, where the processing unit is a line of text, with OBITools the processing unit is a sequence record. In addition, some commands implementing algorithms specific to the processing of DNA metabarcoding data have been added, making <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
|
|
one of the sequence processing tools widely used on UNIX-like systems, suitable for the analysis of DNA metabarcoding data.</p>
|
|
<p><abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
|
|
were originally developed in Python version 2, with some computationally intensive code written in C. They were adapted to the volumes of DNA metabarcoding data generated by 454 pyrosequencing in the early 2000s. With the advent of Solexa and Illumina sequencers, data sizes increased considerably, making OBITools less efficient. Coupled with the switch to Python version 3, OBITools became difficult to implement.</p>
|
|
<p>
|
|
<a href="https://metabarcoding.org/obitools4"><abbr title="The fourth version of the OBITools, a set of unix command line tools for manipulating DNA metabarcoding data">OBITools4</abbr>
|
|
|
|
</a> are the latest version of <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
|
|
. Unlike OBITools3,
|
|
<a href="https://metabarcoding.org/obitools4"><abbr title="The fourth version of the OBITools, a set of unix command line tools for manipulating DNA metabarcoding data">OBITools4</abbr>
|
|
|
|
</a> follow the same philosophy as OBITools1 and OBITools2.
|
|
<a href="https://metabarcoding.org/obitools4"><abbr title="The fourth version of the OBITools, a set of unix command line tools for manipulating DNA metabarcoding data">OBITools4</abbr>
|
|
|
|
</a> are a complete rewrite of the OBITools code in
|
|
<a href="https://go.dev/">GO</a>, an efficient compiled programming language. This language also enables code to be parallelized to take advantage of the multi-core architectures of today’s computers.</p>
|
|
<p>The most important thing to understand about <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
|
|
is that it is not a pipeline for processing DNA metabarcoding data. <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
|
|
are a set of tools that allow you to easily build your own pipeline for processing your DNA metabarcoding data according to your biological questions.</p>
|
|
</article>
|
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<footer class="book-footer">
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<script>(function(){function e(e){const t=window.getSelection(),n=document.createRange();n.selectNodeContents(e),t.removeAllRanges(),t.addRange(n)}document.querySelectorAll("pre code").forEach(t=>{t.addEventListener("click",function(){if(window.getSelection().toString())return;e(t.parentElement),navigator.clipboard&&navigator.clipboard.writeText(t.parentElement.textContent)})})})()</script>
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</footer>
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<div class="book-comments">
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</div>
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<label for="menu-control" class="hidden book-menu-overlay"></label>
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</div>
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<aside class="book-toc">
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<div class="book-toc-content">
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<nav id="TableOfContents">
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<ul>
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<li>
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<ul>
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<li><a href="#what-are-obitools4">What are OBITools4?</a></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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</div>
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</aside>
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</main>
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</body>
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</html>
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