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Subread 比对工具:基于种子投票的快速、准确和可扩展的读段比对。

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.

机构信息

Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.

出版信息

Nucleic Acids Res. 2013 May 1;41(10):e108. doi: 10.1093/nar/gkt214. Epub 2013 Apr 4.

Abstract

Read alignment is an ongoing challenge for the analysis of data from sequencing technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and-vote, for mapping reads to a reference genome. The new strategy chooses the mapped genomic location for the read directly from the seeds. It uses a relatively large number of short seeds (called subreads) extracted from each read and allows all the seeds to vote on the optimal location. When the read length is <160 bp, overlapping subreads are used. More conventional alignment algorithms are then used to fill in detailed mismatch and indel information between the subreads that make up the winning voting block. The strategy is fast because the overall genomic location has already been chosen before the detailed alignment is done. It is sensitive because no individual subread is required to map exactly, nor are individual subreads constrained to map close by other subreads. It is accurate because the final location must be supported by several different subreads. The strategy extends easily to find exon junctions, by locating reads that contain sets of subreads mapping to different exons of the same gene. It scales up efficiently for longer reads.

摘要

读段比对是测序技术数据分析中的一个持续挑战。本文提出了一种优雅简洁的多种子策略,称为种子投票(seed-and-vote),用于将读段映射到参考基因组上。新策略直接从种子中选择读段的映射基因组位置。它使用从每个读段中提取的相对大量的短种子(称为子读段),并允许所有种子对最佳位置进行投票。当读段长度 <160bp 时,使用重叠的子读段。然后使用更传统的比对算法来填充构成获胜投票块的子读段之间的详细错配和插入缺失信息。该策略速度快,因为在进行详细比对之前,整体基因组位置已经选择完毕。它具有敏感性,因为不需要单个子读段精确映射,也不需要单个子读段受其他子读段的限制而靠近映射。它准确性高,因为最终位置必须由几个不同的子读段来支持。该策略通过定位包含映射到同一基因不同外显子的子读段集合的读段,很容易扩展到寻找外显子交界处。对于较长的读段,它可以高效扩展。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffcf/3664803/eaaf1a287c28/gkt214f1p.jpg

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