CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.

ABSTRACT: The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Moreover, even slight improvements in this area are important but challenging, and usually require significantly more computational endeavor. In this paper, we present CUSHAW3, an open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. In this aligner, we have investigated a hybrid seeding approach to improve alignment quality, which incorporates three different seed types, i.e. maximal exact match seeds, exact-match k-mer seeds and variab

SUBMITTER: Liu Y 

PROVIDER: S-EPMC3899341 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature