preprintDROPS (Schloss Dagstuhl – Leibniz Center for Informatics)Mar 16, 2013GREEN OA

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

HLHeng Li
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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: hengli@broadinstitute.org

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Topics & keywords

Topics
Keywords
  • Contig
  • Sequence (biology)
  • clone (Java method)
  • Sequence assembly
  • Computational biology
  • Genetics
  • Biology
  • Computer science
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