This is the command fasta2frag that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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