SRmapper: a fast and sensitive genome-hashing alignment tool
SRmapper: a fast and sensitive genome-hashing alignment tool
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DOI：
10.1093/bioinformatics/bts712
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发表时间：
2013-02-01
期刊：
影响因子：
5.8
通讯作者：
Wong, Chung F.
中科院分区：
文献类型：
--
作者：
Gontarz, Paul M.;Berger, Jennifer;Wong, Chung F.
答：现代测序仪器每天能够产生数百万个短读段。与读段和参考基因组序列之间的变异一起产生的大量读段，所述变异由合理差异（例如单核苷酸多态性和插入/缺失（indel））和测序仪错误引起，使得比对成为困难且计算昂贵的任务，并且许多读段不能被比对。在这里，我们介绍了一种新的比对工具，SRmapper，它在测试中使用真实的数据可以对齐100亿个碱基对从短读到人类基因组每个计算机处理器天。SRmapper比基于Burrows-Wheeler变换的当前程序容忍更高数量的错配，并且根据读取长度在2- 8倍更少的时间内找到大约相同数量的比对（对于更长的读取长度具有更高的性能增益）。当前版本的SRmapper以碱基空间fastq格式对齐单端和双端读数，并以序列对齐/映射格式输出对齐结果。SRmapper使用概率方法来设置允许的错配的默认数量并确定比对质量。SRmapper的内存占用（类似于2.5 GB）足够小，可以在具有4 GB随机存取内存的计算机上运行，用于人类大小的基因组。最后，SRmapper的设计，使其功能可以扩展到寻找小indel以及长缺失和染色体易位在未来的版本。
A: Modern sequencing instruments have the capability to produce millions of short reads every day. The large number of reads produced in conjunction with variations between reads and reference genomic sequences caused both by legitimate differences, such as single-nucleotide polymorphisms and insertions/deletions (indels), and by sequencer errors make alignment a difficult and computationally expensive task, and many reads cannot be aligned. Here, we introduce a new alignment tool, SRmapper, which in tests using real data can align 10s of billions of base pairs from short reads to the human genome per computer processor day. SRmapper tolerates a higher number of mismatches than current programs based on Burrows-Wheeler transform and finds about the same number of alignments in 2-8x less time depending on read length (with higher performance gain for longer read length). The current version of SRmapper aligns both single and pair-end reads in base space fastq format and outputs alignments in Sequence Alignment/Map format. SRmapper uses a probabilistic approach to set a default number of mismatches allowed and determines alignment quality. SRmapper's memory footprint (similar to 2.5 GB) is small enough that it can be run on a computer with 4 GB of random access memory for a genome the size of a human. Finally, SRmapper is designed so that its function can be extended to finding small indels as well as long deletions and chromosomal translocations in future versions.