Haplotype Assembly Refinement & Improvement

Haplotyping is the assignment of polymorphisms to the correct allele(s) in a diploid or polyploid organism. Haplotyping is an especially complex problem that has been little addressed by the current technologies. In particular, current Next-Generation Sequencing (NGS) technologies that use short reads make it difficult to haplotype over long distances. A related complex problem is that of diploid or polyploid assembly, which requires the accurate extension of reads to assemble distinct haplotypes for each allele.

Current sequence assemblers are designed to try and collapse/merge, two or more alleles that may be present in an organism. Applying these assemblers to sequences from diploid or highly polymorphic organisms leads to many problems and misassemblies, which have been well documented, however an effective solution to this problem has not yet been presented. We used a variety of sequencing technologies and tested several different manual haplotyping strategies in order to identify a best strategy for haplotyping. In this poster we present a software tool, which significantly decreases the amount of time spent on manual haplotype phasing of a high-GC content, polymorphic, and diploid organism.