Aligning sequence reads, clone sequences and assembly contigs with BWA MEM
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 this http URL. Contact: hengli@broadinstitute.org