HTSlib: C library for reading/writing high-throughput sequencing data.
HTSlib: C library for reading/writing high-throughput sequencing data.
复制标题
DOI：
10.1093/gigascience/giab007
复制
发表时间：
2021-02-16
期刊：
影响因子：
9.2
通讯作者：
Davies RM
中科院分区：
文献类型：
--
作者：
Bonfield JK;Marshall J;Danecek P;Li H;Ohan V;Whitwham A;Keane T;Davies RM
自从VCF和SAM格式最初发布以来，已经创建了大量软件工具来处理这些数据文件。为了促进这一点，从原始SAMtools实现中产生了一个库，重点关注性能和健壮性。文件格式本身已成为全球基因组学与健康联盟管辖下的国际标准。我们提出了一个软件库，提供程序访问测序比对和变异格式。它诞生于广泛使用的SAMtools和BCFtools应用程序。对原始代码进行了相当大的改进，加上许多新功能，包括更新的访问协议，添加CRAM文件格式，更好的索引和迭代器，以及更好地使用线程。自最初的Samtools版本以来，性能得到了显著提高，BAM读写循环的运行速度提高了5倍，BAM到SAM的转换速度提高了13倍（与Samtools 0.1.19相比，两者都使用了16个线程）。HTSlib的广泛采用已经从GitHub和conda下载了超过100万次。C库已被估计900个GitHub项目直接使用，并已被纳入Perl，Python，Rust和R，通过其他语言显着扩大使用数量。HTSlib是开源的，可以在MIT/BSD许可下从htslib.org免费获得。
Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health. We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading. Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded >1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.
登录
查看更多内容
影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
5.8
作者：
Bonfield, James K.
通讯作者：
Bonfield, James K.
影响因子：
9.2
作者：
Danecek P;Bonfield JK;Liddle J;Marshall J;Ohan V;Pollard MO;Whitwham A;Keane T;McCarthy SA;Davies RM;Li H
通讯作者：
Li H
影响因子：
5.8
作者：
Danecek, Petr;Auton, Adam;Durbin, Richard
通讯作者：
Durbin, Richard