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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