fasta2frag1

Splits a single fasta sequence into several overlapping fragments.

Usage

fasta2frag <options> infile outfile

Overview

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.

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