Faster single-end alignment generation utilizing multi-thread for BWA

Biomed Mater Eng. 2015;26 Suppl 1:S1791-6. doi: 10.3233/BME-151480.


Due to next-generation sequencing (NGS) technology, genome sequencing is able to process much more data at low cost. In NGS data analysis, the mapping of sequences into a reference genome takes the largest amount of time to process. Although the Burrows-Wheeler Aligner (BWA) tool is one of the most widely used open-source software tools to align read sequences, it is still limited in that it does not fully support multi-thread mechanisms during the alignment steps. In this paper, we propose a BWA-MT tool, evolved from BWA but supporting multi-thread computation, designed to fully utilize the underlying multi-core architecture of computing resources. By using multi-thread computation, BWA-MT can significantly shorten the time needed to generate an alignment for single-end read sequences. Meanwhile, it generates an identical Sequence Alignment Map (SAM) result file as BWA. To evaluate BWA-MT, we use an evaluation system equipped with twelve cores and 32 GB memory. As a workload, we used the hg19 human genome reference sequence and various numbers of read sequences from 1M to 40M. In our evaluation, BWA-MT displays up to 3.7 times faster performance and generates an identical SAM result file to BWA. Although the increased speed might be dependent on computing resources, we confirm that BWA-MT is highly efficient and effective.

Keywords: burrow-wheeler aligner (BWA) tool; genome sequencing; multi-thread; next-generation sequencing (NGS).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • Chromosome Mapping / methods*
  • Genome, Human / genetics*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Molecular Sequence Data
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*