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README

readFilter.pl
http://sourceforge.net/projects/readFilter/

 Filter DNA reads in fasta format removing sequences not meeting minimum length and 
 maximum number of N's.  Also can remove sequences not containing QC adapter/barcode 
 sequence.  Coordinately filters associated quality files if present.

 NOTE: Does NOT parse sequences by barcode. The QC sequence feature is meant to remove
 low quality NGS sequences, as sequences with errors in a known primer, adpater, barcode
 sequence tend to be more prone to errors in the remainder of the sequence.

INSTALLATION

 No installation is necessary, but file must be executed on a computer with Perl
 installed (http://www.perl.org/).  Script has been tested on Mac & Linux only.

EXECUTION

 SYNTAX:  readFilter.pl -l length -n maxN  -b ReqSeq -i infile -o outfile

 ARGS:    -l minimum length cutoff (DEFAULT = 300)
          -n maximum number of N's allowed in a valid sequence (DEFAULT=1)
          -b barcode (nucleotide sequence which must occur at start to keep)
          -i input fasta file (quality file is inferred to have same name with '.qual'
          -o output fasta file
Source: README, updated 2011-04-13