read_correction_with_sga - Given a fastq file(s), perform SGA preprocessing and error correction
version 1.160490
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
Andrew J. Page <ap13@sanger.ac.uk>
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
To install Bio::AssemblyImprovement, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::AssemblyImprovement
CPAN shell
perl -MCPAN -e shell install Bio::AssemblyImprovement
For more information on module installation, please visit the detailed CPAN module installation guide.