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< p > Five sequence formats are accepted for input files. < em > Fasta</ em > (< a href = "formats.html#sec-fasta" >< span > Section 3.2</ span ></ a > ) and < em > Fastq</ em > (< a href = "formats.html#sec-fastq" >< span > Section 3.3</ 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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< 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 >
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< 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 >
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< li >< code > --solexa</ code > Decodes quality string according to the Solexa specification. (default: false)</ li >
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