Bio::AssemblyImprovement::Assemble::SGA::IndexAndCorrectReads - Performs SGA error correction on the reads
version 1.160490
Runs SGA index and correct. Results file (by default called _sga_error_corrected.fastq) and intermediate files placed in a temporary directory. This temporary directory is cleaned up when this object goes out of scope. Any script/module wishing to use the results should copy them into a more permanent location.
use Bio::AssemblyImprovement::Assemble::SGA::IndexAndCorrectReads; my $sga_error_corrector = Bio::AssemblyImprovement::Assemble::SGA::IndexAndCorrectReads->new( input_filename => 'my_sga_preprocessed_data.fastq', algorithm => 'ropebwt', threads => 8, kmer_length => 41, sga_exec => '/path/to/sga/script.pl', ); $sga_error_corrector->run(); my $results_file = $sga_corrector->_output_filename();
Run the SGA index and correct commands with the appropriate parameters.
Return the full path to the results file
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.