Haplotype and minimum-chimerism consensus determination using short sequence data.

ABSTRACT:

Background

Assembling haplotypes given sequence data derived from a single individual is a well studied problem, but only recently has haplotype assembly been considered for population-sampled data. We discuss a software tool called Hapler, which is designed specifically for low-diversity, low-coverage data such as ecological samples derived from natural populations. Because such data may contain error as well as ambiguous haplotype information, we developed methods that increase confidence in these assemblies. Hapler also reconstructs full consensus sequences while minimizing and identifying possible chimeric points.

Results

Experiments on simulated data indicate that Hapler is effective at assembling haplotypes from gene-sized alignments of short reads. Further, in our tes

SUBMITTER: O'Neil ST 

PROVIDER: S-EPMC3394418 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature