Lacking alignments? The next-generation sequencing mapper segemehl revisited
Lacking alignments? The next-generation sequencing mapper segemehl revisited
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DOI：
10.1093/bioinformatics/btu146
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发表时间：
2014-07-01
期刊：
影响因子：
5.8
通讯作者：
Hoffmann, Steve
中科院分区：
文献类型：
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作者：
Otto, Christian;Stadler, Peter F.;Hoffmann, Steve
动机：下一代测序已成为分子生物学的重要工具。已经设计了各种方案来研究几乎所有物种和组织的基因组、转录和表观基因组特征。对于这些实验中的大多数，生物信息学分析的第一个关键步骤之一是将读取序列映射到参考基因组。结果：在这里，我们与其他最先进的方法进行了比较，提出了我们的读取校准器Segemhl的完整基准。此外，我们引入了LACK工具来挽救未映射的RNAseq读取，该工具与Segmehl和许多其他频繁使用的拆分读取校准器一起工作。可获得性：LACK与Segomehl一起分发，并可在www.Bioinf.uni-leipzig.de/Software/Segomehl/上免费获得。
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/.