Long read alignment based on maximal exact match seeds

Bioinformatics. 2012 Sep 15;28(18):i318-i324. doi: 10.1093/bioinformatics/bts414.

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: liuy@uni-mainz.de; bertil.schmidt@uni-mainz.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Chromosome Mapping
  • Genome, Human
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Software