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.\" ========================================================================
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.IX Title "Bio::Assembly::IO::bowtie 3pm"
.TH Bio::Assembly::IO::bowtie 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Assembly::IO::bowtie \- An IO module for assemblies in Bowtie format *BETA*
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 4
\& $aio = Bio::Assembly::IO( \-file   => "mybowtie.bowtie",
\&                           \-index  => "myindex",
\&                           \-format => "bowtie");
\& $assy = $aio\->next_assembly;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a read-only \s-1IO\s0 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 \s-1BAM\s0 format taken
by the Bio::Assembly::IO::sam module which in turn uses lstein's
Bio::DB::Sam to parse binary formatted \s-1SAM\s0 (.bam) files guided by a
reference sequence fasta database.
.PP
Some information is lost in conversion from bowtie format to \s-1SAM/BAM\s0 format
that is provided by Bowtie using the \s-1SAM\s0 output option and the conversion
to \s-1SAM\s0 format from bowtie format is slower than using bowtie's \s-1SAM\s0 option.
If you plan to use \s-1SAM/BAM\s0 format it is preferable to use this Bowtie
option rather than convert the format after the fact.
.PP
See the Bio::Assembly::IO::sam documentation for relevant details.
.SH "DETAILS"
.IX Header "DETAILS"
.IP "\(bu" 4
Required files
.Sp
A bowtie (\f(CW\*(C`.bowtie\*(C'\fR) alignment and the bowtie index or fasta
file used to generate the alignment are required.
.IP "\(bu" 4
Compressed files
.Sp
\&...can be specified directly , if IO::Uncompress::Gunzip is
installed. Get it from your local \s-1CPAN\s0 mirror.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
.Vb 1
\&  L<bioperl\-l@bioperl.org>
.Ve
.PP
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Dan Kortschak"
.IX Header "AUTHOR - Dan Kortschak"
Email dan.kortschak adelaide.edu.au
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "\fInew()\fP"
.IX Subsection "new()"
.Vb 5
\& 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
.Ve