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