Bio::AssemblyImprovement::Assemble::SGA::Main - Run SGA preprocess and error correction steps
version 1.160490
Runs SGA preprocess and error correction steps. Final results file made available in current working directory. Intermediate files produced are cleaned up.
use Bio::AssemblyImprovement::Assemble::SGA::Main; my $sga = Bio::AssemblyImprovement::Assemble::SGA::Main->new( input_files => [ $current_dir.'/t/data/forward.fastq', $current_dir.'/t/data/reverse.fastq' ] , algorithm => 'ropebwt', threads => 8, kmer_length => 40, sga_exec => $current_dir.'/t/dummy_sga_script.pl', ); $sga->run(); my $results = $self->_final_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.