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Options to specify input format
-------------------------------
.. program:: obitools
Restrict the analysis to a sub-part of the input file
.....................................................
.. cmdoption:: --skip <N>
The N first sequence records of the file are discarded from the analysis and
not reported to the output file
.. cmdoption:: --only <N>
Only the N next sequence records of the file are analyzed. The following sequences
in the file are neither analyzed, neither reported to the output file.
This option can be used conjointly with the `--skip` option.
Sequence annotated format
.........................
.. cmdoption:: --genbank
Input file is in :doc:`genbank <../genbank>` format.
.. cmdoption:: --embl
Input file is in :doc:`embl <../embl>` format.
:doc:`fasta <../fasta>` related format
.......................................
.. cmdoption:: --fasta
Input file is in :doc:`fasta <../fasta>` format (including
OBITools :doc:`fasta <../fasta>` extensions).
:doc:`fastq <../fastq>` related format
.......................................
.. cmdoption:: --sanger
Input file is in Sanger :doc:`fastq <../fastq>` format (standard
:doc:`fastq <../fastq>` used by HiSeq/MiSeq sequencers).
.. cmdoption:: --solexa
Input file is in :doc:`fastq <../fastq>` format produced by
Solexa (Ga IIx) sequencers.
ecoPCR related format
.....................
.. cmdoption:: --ecopcr
Input file is in :doc:`ecoPCR <../formats>` format.
.. cmdoption:: --ecopcrdb
Input is an :doc:`ecoPCR <../formats>` database.
Specifying the sequence type
............................
.. cmdoption:: --nuc
Input file contains nucleic sequences.
.. cmdoption:: --prot
Input file contains protein sequences.
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