Long read alignment based on maximal exact match seeds.

ABSTRACT: MOTIVATION: The explosive growth of next-generation sequencing datasets poses a challenge to the mapping of reads to reference genomes in terms of alignment quality and execution speed. With the continuing progress of high-throughput sequencing technologies, read length is constantly increasing and many existing aligners are becoming inefficient as generated reads grow larger. RESULTS: We present CUSHAW2, a parallelized, accurate, and memory-efficient long read aligner. Our aligner is based on the seed-and-extend approach and uses maximal exact matches as seeds to find gapped alignments. We have evaluated and compared CUSHAW2 to the three other long read aligners BWA-SW, Bowtie2 and GASSST, by aligning simulated and real datasets to the human genome. The performance evaluation shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads. AVAILABILITY: CUSHAW2, written in C++, and all simulated datasets are available at http://cushaw2.sourceforge.net CONTACT: [e-mail]; [e-mail] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUBMITTER: Liu Y 

PROVIDER: S-EPMC3436841 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature