.TH FASTA2FRAG "1" "June 2013" "3.9.17" "User Commands"
.SH NAME
.B fasta2frag \- splits a single fasta sequence into several overlapping fragments.
.SH DESCRIPTION
This program is part of the MIRA assembler package.  The purpose of fasta2frag
is to fragment sequences into smaller, overlapping
subsequences. It can be used for simulating shotgun sequences. It can create
subsequences in both directions (/default) and also paired-end sequences.
Please check out the
documentation below for more detailed information about fasta2frag.
.SH SYNOPSIS
fasta2frag
\fI<options> infile outfile\fR
.SH OPTIONS
\fB\-l\fR
int      Length of fragments (default=3000)
.TP
\fB\-i\fR
int      Increment of fragment start site (default=2500)
.TP
\fB\-p\fR
int      Paired end (default=0 is off, 1 is on)
.TP
\fB\-P\fR
int      In paired\-end mode, reverse one of the reads
(0 is off, default=1 is on)
.TP
\fB\-s\fR
int      Strobe sequencing (default=0 is off, 1 is on)
.TP
\fB\-q\fR
int      Default quality when no quality data present (default=30)
.TP
\fB\-r\fR
int      Reverse every nth fragment (default=2)
.TP
\fB\-c\fR
int      Circularise fragments so that they form a ring
.IP
(default=0 is is off, 1 would be on)
.TP
\fB\-qualdivisor\fR
int      Divide quality values by this (default=1)
.TP
\fB\-minqual\fR
int      But give it at least this qual (default=0)
.TP
\fB\-insert_size\fR
int      paired\-end: insert size (default=3000)
.TP
\fB\-insert_stdev\fR int
paired\-end: standard dev (default=900)
this is not working at the moment
.TP
\fB\-pairednaming\fR string
naming scheme for paired\-end:
sanger, 454 (default) or solexa
.TP
\fB\-minmut\fR
int      min. number of mutations/seq. errors (def=0)
.TP
\fB\-maxmut\fR
int      max. number of mutations/seq. errors (def=0)
.TP
\fB\-strobeon\fR
int      number of bases read during strobe on
.TP
\fB\-strobeoff\fR
int      number of bases during strobe off
.TP
\fB\-startoffset\fR
int      start at offset position
.TP
\fB\-namesuffix\fR
string   suffix name with string
.SH "SEE ALSO"
A more extensive documentation is provided in the mira-doc package and can be found at
/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
.PP
You can also subscribe one of the MIRA mailing lists at
.IP
http://www.chevreux.org/mira_mailinglists.html
.PP
After subscribing, mail general questions to the MIRA talk mailing list:
.IP
mira_talk@freelists.org
.SH BUGS
To report bugs or ask for features, please use the new ticketing system at:
.IP
http://sourceforge.net/apps/trac/mira\-assembler/
.SH AUTHOR
The author of the mira code is Bastien Chevreux <bach@chevreux.org>
.PP
This manual page was written by Andreas Tille <tille@debian.org> but can be freely used for any other
distribution.