TAPyR v1.3_beta2 (Efficient BWT-based read aligner supporting multiple sequencing platforms)
TAPyR is a read mapper supporting data from multiple sequencing platforms, including Roche 454 GS FLX, Life Technologies Ion Torrent, Illumina HiSeq, etc. It supports both single and paired-end reads, and complies to IO file standards, taking inputs in FASTAQ and SFF formats, and generating SAM files as output. TAPyR uses a custom BWT-based indexing strategy coupled with a seed-and-extend heuristic. The applicaiton has moderate main memory requirements (roughly 1.6x the size of the reference sequence) and has displayed class-leading CPU performance in our tests. The use of the tool is straightforward, requiring minimum user parameterization.