BEDTools: a flexible suite of utilities for comparing genomic features.
BEDTools: a flexible suite of utilities for comparing genomic features.
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DOI：
10.1093/bioinformatics/btq033
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发表时间：
2010-03-15
期刊：
影响因子：
--
通讯作者：
Hall IM
中科院分区：
文献类型：
--
作者：
Quinlan AR;Hall IM
动机：检测不同基因组特征之间的相关性是基因组学研究的一项基本任务。然而，用现有的基于网络的方法搜索特征之间的重叠是复杂的，因为用当前的测序技术常规地产生大量的数据集。因此，需要快速和灵活的工具，以有效的方式询问这些数据的复杂问题。结果如下：本文介绍了一个新的软件套件的比较，操作和注释的基因组特征在浏览器可扩展数据（BED）和通用特征格式（GFF）格式。BEDTools还支持BAM格式的序列比对与BED和GFF功能的比较。这些工具非常有效，允许用户将大型数据集（例如下一代测序数据）与公共和自定义基因组注释轨道进行比较。BEDTools可以相互组合，也可以与标准UNIX命令组合，从而促进常规基因组学任务以及可以快速回答大型基因组数据集复杂问题的管道。可用性和实现：BEDTools是用C++编写的。源代码和全面的用户手册可在http://code.google.com/p/bedtools上免费获取联系方式：aaronquinlan@gmail.com; imh4y@virginia.edu补充信息：补充数据可在在线生物信息学上获取。
Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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DOI：
10.1073/pnas.85.8.2444
发表时间：
1988-04-01
影响因子：
11.1
作者：
PEARSON, WR;LIPMAN, DJ
通讯作者：
LIPMAN, DJ
影响因子：
7
作者：
Giardine, B;Riemer, C;Nekrutenko, A
通讯作者：
Nekrutenko, A
DOI：
10.1093/bioinformatics/btp352
发表时间：
2009-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Handsaker B;Wysoker A;Fennell T;Ruan J;Homer N;Marth G;Abecasis G;Durbin R;1000 Genome Project Data Processing Subgroup
通讯作者：
1000 Genome Project Data Processing Subgroup
影响因子：
7
作者：
Kent, WJ;Sugnet, CW;Haussler, D
通讯作者：
Haussler, D