NAME

Bio::AssemblyImprovement::Assemble::SGA::IndexAndCorrectReads - Performs SGA error correction on the reads

VERSION

version 1.160490

SYNOPSIS

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();

METHODS

run

Run the SGA index and correct commands with the appropriate parameters.

_output_filename

Return the full path to the results file

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