/ 
Bio_AssemblyImprovement-1.160490
River stage zero No dependents
/ read_correction_with_sga

NAME

read_correction_with_sga - Given a fastq file(s), perform SGA preprocessing and error correction

VERSION

version 1.160490

SYNOPSIS

Given a fastq file(s), 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 >
        -fr|shuffled_fastq	   <an interleaved fastq file - 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>
        -a|algorithm		   <indexing algorithm - ropebwt or sais>
        -t|threads	           <number of threads to use for computation. Choose carefully>
        -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 If a zipped name is given like abc.fastq.gz, the results are zipped>
        -d|debug			   <debug>
        -h|help      		   <this message>

Takes in one (interleaved) or 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

# Shuffled fastq file accepted read_correction_with_sga -fr 123_shuffled.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