NAME¶

Bio::Assembly::IO::bowtie - An IO module for assemblies in Bowtie format *BETA*

SYNOPSIS¶

 $aio = Bio::Assembly::IO( -file   => "mybowtie.bowtie",
                           -index  => "myindex",
                           -format => "bowtie");
 $assy = $aio->next_assembly;

DESCRIPTION¶

This is a read-only IO module designed to convert Bowtie (<http://bowtie-bio.sourceforge.net/>) formatted alignments to Bio::Assembly::Scaffold representations, containing Bio::Assembly::Contig and Bio::Assembly::Singlet objects. It is a wrapper that converts the Bowtie format to BAM format taken by the Bio::Assembly::IO::sam module which in turn uses lstein's Bio::DB::Sam to parse binary formatted SAM (.bam) files guided by a reference sequence fasta database.

Some information is lost in conversion from bowtie format to SAM/BAM format that is provided by Bowtie using the SAM output option and the conversion to SAM format from bowtie format is slower than using bowtie's SAM option. If you plan to use SAM/BAM format it is preferable to use this Bowtie option rather than convert the format after the fact.

See the Bio::Assembly::IO::sam documentation for relevant details.

DETAILS¶

• Required files

  A bowtie (".bowtie") alignment and the bowtie index or fasta file used to generate the alignment are required.

• Compressed files

  ...can be specified directly , if IO::Uncompress::Gunzip is installed. Get it from your local CPAN mirror.

FEEDBACK¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  L<bioperl-l@bioperl.org>

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Dan Kortschak¶

Email dan.kortschak adelaide.edu.au

APPENDIX¶

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

 Title   : new
 Usage   : my $obj = new Bio::Assembly::IO::bowtie();
 Function: Builds a new Bio::Assembly::IO object
 Returns : an instance of Bio::Assembly::IO
 Args    : hash of options:
            -file    => bowtie_output_file
            -index   => bowtie_index or fasta_file used to create index
            -no_head => boolean skip SAM header
            -no_sq   => boolean skip SQ lines of SAM header
 Note    : bowtie_output and fasta files may be gzipped