SEQSPLIT

NAME

seqsplit − split seqs into chunks of defined size and overlap

SYNOPSIS

seqsplit [-options] <seqfile>

DESCRIPTION

This manual page documents briefly the seqsplit command.

seqsplit is a program that splits sequences into smaller chunks of defined size and overlap; output a FASTA file.

OPTIONS

−o <file>

Output the new FASTA file to <file>.

−−fragfile <f>

Save one-line-per-frag coord summary file to <f>.

−−informat <s>

Specify sequence file format <s>.

−−length <n>

Set max length of each unique seq frag to <n>.

−−overlap <n>

Set overlap length to <n> (total frag size = length+overlap).

−−shortnames

Use short "frag1" names, not "<src>/<from>-<to>".

LIMITATIONS

Still working in 32 bits -- no sequence can be more than 2 GB in size.

SEE ALSO

afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1), weight(1).

AUTHOR

Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX : 1-314-362-2157
Email: eddy AT genetics DOT wustl DOT edu

This manual page was written by Nelson A. de Oliveira <naoliv AT gmail DOT com>,
for the Debian project (but may be used by others).