Tool:Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem BWA-MEM is the successor of BWA and BWA-SW. It has the following features: Support of query sequences ranged from ~70bp to a few megabases. Except BWA-SW and Last, most read mappers would not work with >5kb query. Fast. Similar to bowtie2 and twice as fast as BWA/BWA-SW/Cushaw2 for 100bp reads. Twice as fast as BWA-SW