Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

Heng Li

3/16/2013

q-bio.GN

Official code: lh3/bwa (1,769 stars, GPL-3.0, last commit 2026-08-07).

Abstract

Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment. The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases. For mapping 100bp sequences, BWA-MEM shows better performance than several state-of-art read aligners to date. Availability and implementation: BWA-MEM is implemented as a component of BWA, which is available at http://github.com/lh3/bwa. Contact: [email protected]

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Code Implementations(1)

lh3/bwaOfficial100%

GPL-3.0

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

1,769580C, C++Jan 14, 20112 months agoGPL-3.0

bioinformaticsfm-indexgenomicssequence-alignment

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Cite this paper

@article{li2013aligning,
  title  = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},
  author = {Heng Li},
  year   = {2013},
  eprint = {1303.3997},
  archivePrefix = {arXiv},
  url    = {https://arxiv.org/abs/1303.3997}
}

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