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BWA-MEM
This algorithm takes both the forward and reverse strands of the reference and forms a BWT index from the combined set. That way, the seeding method can use backtracking of the FM index in the same manner as the regular BWA. However, the presence of both strands in the index can be used to proceed in both 5’ and 3’ directions of a sequence by jumping strand.
http://www.homolog.us/blogs/blog/2013/05/27/bwa-mem-heng-lis-answer-to-bowtie2/
