Benchmarking short sequence mapping tools

摘要: The development of next-generation sequencing instruments has led to the generation millions short sequences in a single run. process aligning these reads reference genome is time consuming and demands fast accurate alignment tools. However, current proposed tools make different compromises between accuracy speed mapping. Moreover, many important aspects are overlooked while comparing performance newly developed tool state art. Therefore, there need for an objective evaluation method that covers all aspects. In this work, we introduce benchmarking suite extensively analyze with respect various provide comparison. We applied our tests on 9 well known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, Novoalign, mrsFAST (mrFAST) using synthetic data real RNA-Seq data. MAQ RMAP based building hash tables reads, whereas remaining indexing genome. reveal strengths weaknesses each tool. results show no outperforms others metrics. Bowtie maintained best throughput most BWA performed better longer read lengths. not restricted mentioned can be further others. still hard problem affected by factors. provided reveals evaluates factors affecting process. Still, tests. end user should clearly specify his needs order choose provides results.