mrsfast-ultra: a compact, SNP-aware mapper for high performance sequencing applications

High throughput sequencing (HTS) platforms gener-ate unprecedented amounts of data that introduce challenges for processing and downstream analy-sis. While tools that report the ‘best ’ mapping loca-tion of each read provide a fast way to process HTS data, they are not suitable for many types of down-stream analysis such as structural variation detec-tion, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrs-FAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new an