/ 
Bio_AssemblyImprovement-1.130780
/ read_correction_with_sga

NAME

read_correction_with_sga - Given two fastq files (forward and reverse), try and correct the reads using SGA before doing the assembly

VERSION

version 1.130780

SYNOPSIS

Given two input fastq files, perform error correction on them. The results are put into a fastq file called _sga_error_corrected.fastq in the current working directory (or, if specified, a directory of your choice).

Usage: read_correction_with_sga [options]

		-f|forward_fastq       <forward reads file - zipped or unzipped>
        -r|reverse_fastq       <reverse reads files - zipped or unzipped >
        -s|sga_exec	 		   <path to sga script>
        
        -m|min_length	       <discard sequences that are shorter than this during preprocess>
        -q|quality_trim	       <trim reads using Heng Li's BWT trimming algorithm>
        -l|quality_filter	   <discard read if it contains more than this many low-quality bases>
        
        -a|algorithm		   <indexing algorithm - ropebwt or sais>
        -t|threads	           <number of threads to use for computation. Choose carefully>
        -i|disk				   <for disk based index algorithm>
        -h|kmer_threshold	   <kmer threshold. Attempt to correct kmers that appear less than this many times>
        -k|kmer_length	       <the length of kmer to be used>
        -o|output_directory	   <output directory for results file>
        -z|output_filename	   <name of output filename if not using default of _sga_error_corrected.fastq.gz>
        -d|debug			   <debug>
        -h|help      		   <this message>

Takes in two FASTQ files (forward and reverse), and then performs read correction using SGA

# outputs a file called _sga_error_corrected.fastq read_correction_with_sga -f 123_1.fastq -r 123_2.fastq

# Gzipped input files are accepted read_correction_with_sga -f 123_1.fastq.gz -r 123_2.fastq.gz

# This help message read_correction_with_sga -h

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