BEDTools

BEDTools: a flexible suite of utilities for comparing genomic features. 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


References in zbMATH (referenced in 12 articles )

Showing results 1 to 12 of 12.
Sorted by year (citations)

  1. Li, Wentian; Thanos, Dimitrios; Provata, Astero: Quantifying local randomness in human DNA and RNA sequences using Erdös motifs (2019)
  2. Mayura N. Patwardhan, Craig D. Wenger, Eric S. Davis, Douglas H. Phanstiel: Bedtoolsr: An R package for genomic data analysis and manipulation (2019) not zbMATH
  3. Neo Christopher Chung, Błażej Miasojedow, Michał Startek, Anna Gambin: Jaccard/Tanimoto similarity test and estimation methods (2019) arXiv
  4. Robinson, Peter N.; Piro, Rosario Michael; Jäger, Marten: Computational exome and genome analysis (2018)
  5. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  6. Polishko, Anton; Hasan, Md. Abid; Pan, Weihua; Bunnik, Evelien M.; Le Roch, Karine; Lonardi, Stefano: ThIEF: finding genome-wide trajectories of epigenetics marks (2017)
  7. Shomroni, Orr: Development of algorithms and next-generation sequencing data workflows for the analysis of gene regulatory networks (2017)
  8. Mathé, Ewy (ed.); Davis, Sean (ed.): Statistical genomics. Methods and protocols (2016)
  9. Mazza, Tommaso; Castellana, Stefano: Multi-sided compression performance assessment of ABI SOLiD WES data (2013)
  10. Shen, L., Shao, N.-Y., Liu, X., Maze, I., Feng, J., Nestler, E. J. : diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates (2013) not zbMATH
  11. Cox, Anthony J.; Jakobi, Tobias; Rosone, Giovanna; Schulz-Trieglaff, Ole B.: Comparing DNA sequence collections by direct comparison of compressed text indexes (2012)
  12. Quinlan, Aaron R.; Hall, Ira M.: Bedtools: a flexible suite of utilities for comparing genomic features (2010) ioport