NAME

remove_primers_with_quasr - Given a forward and reverse FASTQ file and a file with primers, it will remove the primers if it appears within a specified distance from the beginning of the read

VERSION

version 1.160490

SYNOPSIS

Given a forward & reverse fastq file and a file with primers, it will remove the primers if they appear within a specified distance from the beginning of the read

Usage: remove_primers_with_quasr [options]

                -f|forward_file        <forward fastq file - zipped or unzipped>
                -r|reverse_file            <reverse fastq file - zipped or unzipped>
        -o|output_directory        <Directory to place output file. Default current working directory>
        -p|primers_file            <path to a file containing primers and their reverse complements>
        -L|leeway                          <maximum distance primer can be within a read. Default 5>
        -m|minimum_length          <minimum read length cut off. Default 50>
        -l|median_quality          <median read quality cut off. Default 30>
        -e|quasr_exec              <path to quasr jar file. Default to pathogen installation>
        -d|debug                           <debug>
        -h|help                    <this message>

Takes in a forward and reverse fastq file and a file with primers, and removes the primers that appear within a specified distance in the reads

# outputs files called primer_removed.forward.fastq.gz and primer_removed.reverse.fastq.gz in current working directory remove_primers_with_quasr -f forward.fastq -r reverse.fastq -p /path/to/primers.txt

AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007