  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.
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