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Andrew Page > Bio-VertRes-Config-1.133090 > Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingBowtie2

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NAME ^

Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingBowtie2 - Standard snp calling pipeline for bacteria

VERSION ^

version 1.133090

SYNOPSIS ^

Standard snp calling pipeline for bacteria. Register study, QC, map with bwa, snp call use Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingBowtie2;

   my $obj = Bio::VertRes::Config::Recipes::BacteriaSnpCallingUsingBowtie2->new( 
     database => 'abc', 
     limits => {project => ['Study ABC']}, 
     reference => 'ABC', 
     reference_lookup_file => '/path/to/refs.index'
     );
   $obj->create;

AUTHOR ^

Andrew J. Page <ap13@sanger.ac.uk>

COPYRIGHT AND LICENSE ^

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007
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