NAME

Bio::AssemblyImprovement::Assemble::SGA::PreprocessReads - Preprocess reads before error correction

VERSION

version 1.160490

SYNOPSIS

Runs SGA step to preprocess reads. The preprocessed reads will be in a file called _sga_preprocessed.fastq in a temporary directory (unless an alternative file name is provided). When this object goes out of scope this temporary directory will be cleaned up. Any module/script wishing to use these results should move them to desired location.

   use Bio::AssemblyImprovement::Assemble::SGA::PreprocessReads;

   my $sga_preprocessor = Bio::AssemblyImprovement::Assemble::SGA::PreprocessReads->new(
            input_files     => [ 'forward.fastq', 'reverse.fastq.gz' ] ,
            output_filename => 'mypreprocessedreads.fastq',
            sga_exec        => 'path/to/sga_script.pl',
   );
   
   $sga_preprocessor->run();
   my $preprocessed_file = $sga_preprocessor->_output_filename();

METHODS

_prepare_input_files

Unzip input files if needed

run

Run sga preprocess on the input data.

_output_filename

Return 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