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Overview
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Introgression Populations
Homoeolog-specific Profiling
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Download PolyCat pipeline

Read mapping is a fundamental part of next-generation genomic research and is complicated by genome duplication of many plants. PolyCat is a pipeline for mapping and read categorization of next-generation sequence data produced from allopolyploid organisms including whole genome shotgun, RNA-seq, and bisulfite-treated reads. It is written in C++ and Perl and needs the following programs and libraries installed:
            
  • Samtools (samtools.sourceforge.net)
  • Bamtools (github.com/pezmaster31/bamtools)
  • BioPerl (bioperl.org)
  • Bio::DB::SAM perl module
    (search.cpan.org/~lds/Bio-SamTools-1.37/lib/Bio/DB/Sam.pm)
We also recommend the use of the following (but polyCat can handle any BAM file):
            
  • Sickle (github.com/najoshi/sickle)
  • GSNAP (research-pub.gene.com/gmap)
The PolyCat package and D-genome files, required for Gossypium related applications, can be downloaded at the following links.
            



We welcome your comments and suggestions.