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Reorganization of the documentation book directory

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Eric Coissac
2023-02-23 23:41:24 +01:00
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# Specifying the data input to *OBITools* commands
## Specifying input format
Five sequence formats are accepted for input files. *Fasta* (@sec-fasta) and *Fastq* (@sec-fastq) 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 *OBITools* and allows to read *ecoPCR* outputs as sequence files.
- `--ecopcr` : Read data following the *ecoPCR* output format.
- `--embl` Read data following the *EMBL* flatfile format.
- `--genbank` Read data following the *Genbank* flatfile format.
Several encoding schemes have been proposed for quality scores in *Fastq* format. Currently, *OBITools* considers Sanger encoding as the standard. For reasons of compatibility with older datasets produced with *Solexa* sequencers, it is possible, by using the following option, to force the use of the corresponding quality encoding scheme when reading these older files.
- `--solexa` Decodes quality string according to the Solexa specification. (default: false)