mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
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DOI：
10.1093/nar/gku370
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发表时间：
2014-07
影响因子：
14.9
通讯作者：
Sahinalp SC
中科院分区：
文献类型：
--
作者：
Hach F;Sarrafi I;Hormozdiari F;Alkan C;Eichler EE;Sahinalp SC
高通量测序（HTS）平台产生了前所未有的数据量，这给处理和下游分析带来了挑战。虽然报告每个读段的“最佳”映射位置的工具提供了处理HTS数据的快速方法，但它们不适用于许多类型的下游分析，例如结构变异检测，其中报告每个读段的多个映射基因座是重要的。为此，我们引入了mrsFAST-Ultra，一种快速的，高速缓存无关的，SNP感知的对齐器，可以非常有效地处理HTS读取的多映射。mrsFAST-Ultra改进了mrsFAST，我们的第一个缓存无关读对齐器，能够处理多映射读取，通过新的紧凑的索引结构，不仅减少了整体内存使用，而且减少了每次对齐的CPU操作数量。事实上，mrsFAST-Ultra生成的索引大小比mrsFAST小10倍。同样重要的是，mrsFAST-Ultra引入了新的特征，例如能够（i）获得每个读段的最佳映射基因座，以及（ii）对于任何用户指定的n，返回具有至多n个映射基因座（在误差阈值内）的所有读段以及这些基因座。此外，mrsFAST-Ultra是SNP感知的，即它可以将读数映射到参考基因组，同时排除db-SNP提供的常见SNP位置处发生的错配;这显著增加了可以映射到参考基因组的读数的数量。请注意，上述所有功能都是在索引结构中实现的，并不是简单的后处理步骤，因此可以高效地执行。最后，mrsFAST-Ultra利用多个可用的内核和处理器，并可针对各种内存设置进行调整。我们的研究结果表明，mrsFAST-Ultra的速度大约是其前身mrsFAST的五倍。与新增强的流行工具（如Bowtie 2）相比，它更敏感（每次读取可以报告10次或更多次映射），并且在多映射模式下速度更快（6次或更多次）。此外，mrsFAST-Ultra对整个人类参考基因组的索引大小为2GB，大约是Bowtie 2的一半。mrsFAST-Ultra是开源的，可以在http://mrsfast.sourceforge.net上访问。
High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the ‘best’ mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such as structural variation detection, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. In fact the size of the index generated by mrsFAST-Ultra is 10 times smaller than that of mrsFAST. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNP-aware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. Notice that all of the above features are implemented within the index structure and are not simple post-processing steps and thus are performed highly efficiently. Finally, mrsFAST-Ultra utilizes multiple available cores and processors and can be tuned for various memory settings. Our results show that mrsFAST-Ultra is roughly five times faster than its predecessor mrsFAST. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or more) in the multi-mapping mode. Furthermore, mrsFAST-Ultra has an index size of 2GB for the entire human reference genome, which is roughly half of that of Bowtie2. mrsFAST-Ultra is open source and it can be accessed at http://mrsfast.sourceforge.net.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
30.8
作者：
Alkan, Can;Kidd, Jeffrey M.;Marques-Bonet, Tomas;Aksay, Gozde;Antonacci, Francesca;Hormozdiari, Fereydoun;Kitzman, Jacob O.;Baker, Carl;Malig, Maika;Mutlu, Onur;Sahinalp, S. Cenk;Gibbs, Richard A.;Eichler, Evan E.
通讯作者：
Eichler, Evan E.
影响因子：
5.8
作者：
Gontarz, Paul M.;Berger, Jennifer;Wong, Chung F.
通讯作者：
Wong, Chung F.
DOI：
10.1093/bioinformatics/btq216
发表时间：
2010-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Hormozdiari F;Hajirasouliha I;Dao P;Hach F;Yorukoglu D;Alkan C;Eichler EE;Sahinalp SC
通讯作者：
Sahinalp SC
影响因子：
5.8
作者：
Hormozdiari, Farhad;Hach, Faraz;Alkan, Can
通讯作者：
Alkan, Can