Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 May 1;30(9):1290-1.
doi: 10.1093/bioinformatics/btt756. Epub 2014 Jan 5.

CGAT: computational genomics analysis toolkit

David Sims  1 , Nicholas E Ilott, Stephen N Sansom, Ian M Sudbery, Jethro S Johnson, Katherine A Fawcett, Antonio J Berlanga-Taylor, Sebastian Luna-Valero, Chris P Ponting, Andreas Heger
Affiliations

CGAT: computational genomics analysis toolkit

David Sims et al. Bioinformatics. .

Abstract

Computational genomics seeks to draw biological inferences from genomic datasets, often by integrating and contextualizing next-generation sequencing data. CGAT provides an extensive suite of tools designed to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Visualization of the output of (a) bam2geneprofile and (b) bam2peakshape
See this image and copyright information in PMC

References

    1. Behnel S, et al. Cython: the best of both worlds. Comput. Sci. Eng. 2011;13:31–39.
    1. ENCODE Project Consortium et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;7414:57–74. - PMC - PubMed
    1. Feng J, et al. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 2012;7:1728–1740. - PMC - PubMed
    1. Goecks J, et al. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11:R86. - PMC - PubMed
    1. Harrow J, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22:1760–1774. - PMC - PubMed

Publication types