NAME - Extract subsequence from a (multi) Fasta file

SYNOPSIS [--fa FILE] [-s INT] [-e INT] [-id STRING] [--strand +/-]


Extract a subsequence from a (multi) Fasta file. Interval coordinates are passed as start and end coordinates via the -s and -e options, respectively. Output is written to STDOUT.



Input file in Fasta format (mandatory)


Start of the sequence interval to extract


End of the sequence interval to extract


Fasta ID of the sequence to extract from. This is only required for multi Fasta input files.


Specify the strand to extract sequence data from. Allowed arguments are + amd -. In the latter case, retrieve reverse complement of the sequence interval from start to end.

--help -h

Print short help


Prints the manual page and exits


Michael T. Wolfinger <>