NAME

shredFasta.pl

SYNOPSIS

  shredFasta.pl [options] <fastaFile> <outputFile>
  Options:
  -l <number>           Fragment length (required)
  -o <number>           Fragment overlapping length (required)
  -q                    Specify this if <fastaFile> is the quality file
  -qmax <number>        In conjunction with the -q option, specify the maximum
                        consensus qualtiy (optional)
  -qoverlap <number>    In conjunction with the -q option, specify the maximum qualtiy
                        value at overlapping ends (optional)
  -h                    Help message (optional)

DESCRIPTION

This script is used to chop sequences within a fasta file into overlapping fragments. A fasta containing multiple entries is allowed. Each fragment is separated by a fasta header tag named using the original read name with an iteration number appened to the end (using a '_' delimiter).

$Revision: 1.4 $

$Date: 2009-10-08 17:26:38 $

AUTHOR(S)

Stephan Trong

HISTORY