NAME

Bio::AssemblyImprovement::Assemble::SGA::Main - Run SGA preprocess and error correction steps

VERSION

version 1.160490

SYNOPSIS

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;

METHODS

run

SEE ALSO

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