Abstract Detail

Genomics / Proteomics

Olsen, Christian [1], Qaadri, Kashef [2], Hsiau, Tim [3], Brubaker, Shane [3].

Haplotyping Assembly Refinement and Improvement II.

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 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. In this poster using Geneious R7 we present an efficient scalable strategy to assemble and haplotype a very high-GC, polymorphic, diploid organism.

1 - Biomatters, Application Scientists, 60 Park Place, Suite 2100, Newark, NJ, 07102, United States
2 - Biomatters, VP Sales, 60 Park Place, Suite 2100, Newark, NJ, 07102, United States
3 - Solazyme, Inc., Scientist, 225 Gateway Blvd., South San Francisco, CA, 94080

Keywords:
Haplotyping
Bioinformatics.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Eyrie/Boise Centre
Date: Monday, July 28th, 2014
Time: 5:30 PM
Number: PGP006
Abstract ID:586
Candidate for Awards:None