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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

-h

Help; display usage and version.

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