BEDTools helps you find out "things" that overlap in the genome
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Denis Jacob Machado
Mar 25, 2015, 11:27:25 AM3/25/15
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A Twitter from Sumit Middha (@bioinfosm) earlier today statated that "Most bioinformaticians to be replaced by BEDTools.. or better #bioinformatics using BEDTools ;)". Actually, this was a response to another Twitter by The Science Web (@TheScienceWeb) which said that "Most bioinformaticians to be replaced by BEDTools" (see full blog post here http://wp.me/p4ik2k-4c).
BEDTools is a suite of software tools that help you find out things that overlap in the genome, which comprises most of the job of most bioinformaticians nowadays.
Official package description
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
Project URLs
http://bedtools.readthedocs.org/en/latest/
https://github.com/arq5x/bedtools2
References
Dale, R. K., Pedersen, B. S., & Quinlan, A. R. (2011). Pybedtools: A flexible Python library for manipulating genomic datasets and annotations. Bioinformatics, 27(24), 3423–3424. doi:10.1093/bioinformatics/btr539
Quinlan, A. R. (2014). BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] (pp. 1–34). doi:10.1002/0471250953.bi1112s47
Quinlan, A. R., & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841–842. doi:10.1093/bioinformatics/btq033
BEDTools is a suite of software tools that help you find out things that overlap in the genome, which comprises most of the job of most bioinformaticians nowadays.
Official package description
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
Project URLs
http://bedtools.readthedocs.org/en/latest/
https://github.com/arq5x/bedtools2
References
Dale, R. K., Pedersen, B. S., & Quinlan, A. R. (2011). Pybedtools: A flexible Python library for manipulating genomic datasets and annotations. Bioinformatics, 27(24), 3423–3424. doi:10.1093/bioinformatics/btr539
Quinlan, A. R. (2014). BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] (pp. 1–34). doi:10.1002/0471250953.bi1112s47
Quinlan, A. R., & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841–842. doi:10.1093/bioinformatics/btq033
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