question: Which NGS alignment software implement the Burrows-Wheeler Transform?
answer: The most widely used software belong to the family of the Burrows-Wheeler Aligner (BWA) and its variants for local alignment BWASW, map reduce BWASW-PMR and multi-threaded implementation BWA-MT. Other approaches include Bowtie, SOAP2, BWBBLE, SOAP2 and FANSe2.