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BWA^3,4 (Version 0.7.12) - Uses a Burrows-Wheeler transform to create an index of the genome.  Handles gapped alignments and ambiguous bases (N’s).  BWA-backtrack may uses a backward search  may be optimal for short reads (>70bp).  BWA-MEM typically fastest and most accurate for longer reads, although BWA-SW may have better sensitivity when gapped alignments.  Popular for DNA-seq variant calling pipelines, but not for RNA-seq as splicing is not taken into account. (http://bio-bwa.sourceforge.net/) 

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