fasta2frag (1)

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)

-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

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:

• [email protected]

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

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

The author of the mira code is Bastien Chevreux <[email protected]>

This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other distribution.