title: Faster single-end alignment generation utilizing multi-thread for BWA.
abstract: 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.
authors.affiliation: Department of Information Technology, Chonbuk National University, Republic of Korea.
authors.forename: Heeseung
authors.initials: H
authors.lastname: Jo
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Republic of Korea.
authors.forename: Gunhwan
authors.initials: G
authors.lastname: Koh
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: burrow-wheeler aligner (BWA) tool; genome sequencing; multi-thread; next-generation sequencing (NGS)