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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 (
  • Bamtools (
  • BioPerl (
  • Bio::DB::SAM perl module
We also recommend the use of the following (but polyCat can handle any BAM file):
  • Sickle (
  • GSNAP (
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.