hts-nim: scripting high-performance genomic analyses
hts-nim: scripting high-performance genomic analyses
复制标题
hts-nim：编写高性能基因组分析脚本
DOI：
10.1101/261735
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发表时间：
2018
期刊：
影响因子：
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通讯作者：
A. Quinlan
中科院分区：
文献类型：
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作者：
Brent S. Pedersen;A. Quinlan
动机从基因组数据中提取生物学见解不可避免地需要定制软件。在许多情况下，这是通过脚本语言来完成的，因为它们的可访问性和简洁性。不幸的是，脚本语言的易用性通常会带来巨大的性能成本，这对于现代基因组数据集的规模来说尤其严重。结果 我们提出了 hts-nim，这是一个用 Nim 编程语言编写的高性能库，它提供了简单的、类似脚本的语法，而不牺牲性能。可用性 hts-nim 位于 https://github.com/brentp/hts-nim，示例工具位于 https://github.com/brentp/hts-nim-tools，两者均获得 MIT 许可。联系 bpederse@gmail.com 补充信息 补充数据可在生物信息学在线获取。
Motivation Extracting biological insight from genomic data inevitably requires custom software. In many cases, this is accomplished with scripting languages, owing to their accessibility and brevity. Unfortunately, the ease of scripting languages typically comes at a substantial performance cost that is especially acute with the scale of modern genomics datasets. Results We present hts-nim, a high-performance library written in the Nim programming language that provides a simple, scripting-like syntax without sacrificing performance. Availability hts-nim is available at https://github.com/brentp/hts-nim and the example tools are at https://github.com/brentp/hts-nim-tools both under the MIT license. Contact bpederse@gmail.com Supplementary information Supplementary data are available at Bioinformatics online.