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< h2 data-number = "4.1" class = "anchored" data-anchor-id = "specifying-input-format" > < span class = "header-section-number" > 4.1< / span > Specifying input format< / h2 >
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< p > Five sequence formats are accepted for input files. < em > Fasta< / em > (< a href = "formats.html#sec-fasta" > < span > Section 2.1.2< / span > < / a > ) and < em > Fastq< / em > (< a href = "formats.html#sec-fastq" > < span > Section 2.1.3< / span > < / a > ) are the main ones, EMBL and Genbank allow the use of flat files produced by these two international databases. The last one, ecoPCR, is maintained for compatibility with previous < em > OBITools< / em > and allows to read < em > ecoPCR< / em > outputs as sequence files.< / p >
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< ul >
< li > < code > --ecopcr< / code > : Read data following the < em > ecoPCR< / em > output format.< / li >
< li > < code > --embl< / code > Read data following the < em > EMBL< / em > flatfile format.< / li >
< li > < code > --genbank< / code > Read data following the < em > Genbank< / em > flatfile format.< / li >
< / ul >
< p > Several encoding schemes have been proposed for quality scores in < em > Fastq< / em > format. Currently, < em > OBITools< / em > considers Sanger encoding as the standard. For reasons of compatibility with older datasets produced with < em > Solexa< / em > sequencers, it is possible, by using the following option, to force the use of the corresponding quality encoding scheme when reading these older files.< / p >
< ul >
< li > < code > --solexa< / code > Decodes quality string according to the Solexa specification. (default: false)< / li >
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