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SAMtools 和 BCFtools 十二年。

Twelve years of SAMtools and BCFtools.

机构信息

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1QH, UK.

出版信息

Gigascience. 2021 Feb 16;10(2). doi: 10.1093/gigascience/giab008.

DOI:10.1093/gigascience/giab008
PMID:33590861
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7931819/
Abstract

BACKGROUND: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. CONCLUSION: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.

摘要

背景：SAMtools 和 BCFtools 是广泛用于处理和分析高通量测序数据的程序。它们包括用于文件格式转换和操作、排序、查询、统计、变异调用和效应分析等方法的工具。

发现：第一个版本于 12 年前在线出现，此后一直得到维护和进一步开发，多年来添加了许多新功能和改进。SAMtools 和 BCFtools 包代表了一组独特的工具，这些工具已被用于许多其他软件项目和无数的基因组管道中。

结论：SAMtools 和 BCFtools 都可以在 GitHub 上根据许可协议免费获取，无论是非商业还是商业用途都可以免费使用。这两个包都通过 Bioconda 被安装了超过 100 万次。源代码和文档可从 https://www.htslib.org 获得。

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本文引用的文献

[1]
HTSlib: C library for reading/writing high-throughput sequencing data.

Gigascience. 2021-2-16

[2]
Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data.

Plants (Basel). 2020-4-2

[3]
Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data.

Genome Biol. 2019-11-19

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Crumble: reference free lossy compression of sequence quality values.

Bioinformatics. 2019-1-15

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Bioconda: sustainable and comprehensive software distribution for the life sciences.

Nat Methods. 2018-7

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BCFtools/csq: haplotype-aware variant consequences.

Bioinformatics. 2017-7-1

[7]
The Ensembl Variant Effect Predictor.

Genome Biol. 2016-6-6

[8]
A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.

PLoS One. 2016-5-13

[9]
BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.

Bioinformatics. 2016-6-1

[10]
Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error.

BMC Res Notes. 2015-12-8

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