Lacking alignments? The next-generation sequencing mapper segemehl revisited

Motivation: Next-generation sequencing has become an important tool in molecular biology. Various protocols to investigate genomic, transcriptomic and epigenomic features across virtually all species and tissues have been devised. For most of these experiments, one of the first crucial steps of bioinformatic analysis is the mapping of reads to reference genomes. Results: Here, we present thorough benchmarks of our read aligner segemehl in comparison with other state-of-the-art methods. Furthermore, we introduce the tool lack to rescue unmapped RNAseq reads which works in conjunction with segemehl and many other frequently used split-read aligners. Availability: lack is distributed together with segemehl and freely available at www.bioinf.uni-leipzig.de/Software/ segemehl/.