xenial (1) fasta2frag.1.gz

Provided by: mira-assembler_4.9.5-5_amd64 bug

NAME

       fasta2frag - splits a single fasta sequence into several overlapping fragments.

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.

SYNOPSIS

       fasta2frag <options> infile outfile

OPTIONS

       -l int      Length of fragments (default=3000)

       -i     int      Increment of fragment start site (default=2500)

       -p     int      Paired end (default=0 is off, 1 is on)

       -P     int      In paired-end mode, reverse one of the reads (0 is off, default=1 is on)

       -s     int      Strobe sequencing (default=0 is off, 1 is on)

       -q     int      Default quality when no quality data present (default=30)

       -r     int      Reverse every nth fragment (default=2)

       -c     int      Circularise fragments so that they form a ring

              (default=0 is is off, 1 would be on)

       -qualdivisor
              int      Divide quality values by this (default=1)

       -minqual
              int      But give it at least this qual (default=0)

       -insert_size
              int      paired-end: insert size (default=3000)

       -insert_stdev int
              paired-end: standard dev (default=900) this is not working at the moment

       -pairednaming string
              naming scheme for paired-end: sanger, 454 (default) or solexa

       -minmut
              int      min. number of mutations/seq. errors (def=0)

       -maxmut
              int      max. number of mutations/seq. errors (def=0)

       -strobeon
              int      number of bases read during strobe on

       -strobeoff
              int      number of bases during strobe off

       -startoffset
              int      start at offset position

       -namesuffix
              string   suffix name with string

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.

       You can also subscribe one of the MIRA mailing lists at

              http://www.chevreux.org/mira_mailinglists.html

       After subscribing, mail general questions to the MIRA talk mailing list:

              mira_talk@freelists.org

BUGS

       To report bugs or ask for features, please use the new ticketing system at:

              http://sourceforge.net/apps/trac/mira-assembler/

AUTHOR

       The author of the mira code is Bastien Chevreux <bach@chevreux.org>

       This  manual  page  was  written by Andreas Tille <tille@debian.org> but can be freely used for any other
       distribution.