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.