Hobbes: optimized gram-based methods for efficient read alignment.
Hobbes: optimized gram-based methods for efficient read alignment.
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DOI：
10.1093/nar/gkr1246
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发表时间：
2012-03
影响因子：
14.9
通讯作者：
Xie X
中科院分区：
文献类型：
--
作者：
Ahmadi A;Behm A;Honnalli N;Li C;Weng L;Xie X
测序技术的最新进展使得能够以相对低的成本快速生成数十亿个碱基。许多测序应用中至关重要的第一步是将这些读数映射到参考基因组。然而，当参考基因组很大时，由于读取的绝对量，并且因为许多读取近似但不精确地映射到参考序列，找到准确的映射构成了显著的计算挑战。我们介绍霍布斯，一个新的基于语法的程序对齐短读，支持汉明和编辑距离。霍布斯实现了两种新的技术，产生实质性的性能改进：一个优化的语法选择程序读取，和一个高速缓存高效过滤器修剪候选映射。我们系统地测试了Hobbes在读取长度从35到100 bp变化的真实的和模拟数据上的性能，并将其性能与几种最先进的读取映射程序进行了比较，包括Bowtie，BWA，mrsFast和RazerS。Hobbes比我们测试过的所有其他读取映射程序都要快，同时保持高映射质量。Hobbes比Bowtie快约5倍，比BWA快约2-10倍，这取决于读取长度和错误率，当被要求分别在给定的汉明或编辑距离内找到人类基因组中读取的所有映射位置时。Hobbes支持SAM输出格式，并在http://hobbes.ics.uci.edu上公开提供。
Recent advances in sequencing technology have enabled the rapid generation of billions of bases at relatively low cost. A crucial first step in many sequencing applications is to map those reads to a reference genome. However, when the reference genome is large, finding accurate mappings poses a significant computational challenge due to the sheer amount of reads, and because many reads map to the reference sequence approximately but not exactly. We introduce Hobbes, a new gram-based program for aligning short reads, supporting Hamming and edit distance. Hobbes implements two novel techniques, which yield substantial performance improvements: an optimized gram-selection procedure for reads, and a cache-efficient filter for pruning candidate mappings. We systematically tested the performance of Hobbes on both real and simulated data with read lengths varying from 35 to 100 bp, and compared its performance with several state-of-the-art read-mapping programs, including Bowtie, BWA, mrsFast and RazerS. Hobbes is faster than all other read mapping programs we have tested while maintaining high mapping quality. Hobbes is about five times faster than Bowtie and about 2–10 times faster than BWA, depending on read length and error rate, when asked to find all mapping locations of a read in the human genome within a given Hamming or edit distance, respectively. Hobbes supports the SAM output format and is publicly available at http://hobbes.ics.uci.edu.
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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：
2.5
作者：
Xiao, Chuan;Wang, Wei;Lin, Xuemin
通讯作者：
Lin, Xuemin
影响因子：
3
作者：
Smith AD;Xuan Z;Zhang MQ
通讯作者：
Zhang MQ
影响因子：
7
作者：
Li, Heng;Ruan, Jue;Durbin, Richard
通讯作者：
Durbin, Richard
影响因子：
7
作者：
Ning, ZM;Cox, AJ;Mullikin, JC
通讯作者：
Mullikin, JC