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


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.


fasta2frag <options> infile outfile


-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)

int Divide quality values by this (default=1)

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

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

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

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

int number of bases read during strobe on

int number of bases during strobe off

int start at offset position

string suffix name with string

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