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.
Here, a team led by researchers at the University Leipzig, Germany present thorough benchmarks of the read aligner segemehl in comparison with other state-of-the-art methods. Furthermore, they introduce the tool lack to rescue unmapped RNA-seq 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/