SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.
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DOI：
10.1099/mgen.0.000056
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发表时间：
2016-04
影响因子：
3.9
通讯作者：
Harris SR
中科院分区：
文献类型：
--
作者：
Page AJ;Taylor B;Delaney AJ;Soares J;Seemann T;Keane JA;Harris SR
基因组测序成本的迅速下降导致原核群体研究中使用的样本数量成比例增加。从大型全基因组比对中提取单核苷酸多态性 (SNP) 现在已成为一项常规任务，但现有工具无法随着研究规模的增加而有效扩展。这些工具速度慢、内存效率低，并且是通过非标准程序安装的。我们提出的 SNP 位点可以使用适度的资源从多 FASTA 比对中快速提取 SNP，并可以以多种格式输出结果以供下游分析。使用 59 MB RAM 和 1 个 CPU 核心，可以在 267 秒内从 8.3 GB 比对文件（1842 个分类单元、22 618 个位点）中提取 SNP，从而可以在普通计算机上运行。它可以通过 Debian 和 Homebrew 包管理器轻松安装，并已在 20 多个操作系统上成功进行了测试。 SNP-sites 用 C 语言实现，可在开源许可证 GNU GPL 版本 3 下使用。
Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1842 taxa, 22 618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. It is easy to install through the Debian and Homebrew package managers, and has been successfully tested on more than 20 operating systems. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.