BRAT 1.2.4 / BRAT-BW 2.0.1 / BRAT-nova – Bayesian Modeling of Recombination Events

BRAT 1.2.4 / BRAT-BW 2.0.1 / BRAT-nova

:: DESCRIPTION

BRAT contains an implementation of a Bayesian model-based method for detecting recombination events in bacterial populations using DNA sequence data.

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BRAT-BW is a fast, accurate and memory-efficient tool that maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows-Wheeler transform).

BRAT-nova is a novel optimized versatile aligner that is accurate and fast. BRAT-nova is faster than BRAT-BW. BRAT-nova maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows-Wheeler transform). The package includes tools for trimming low quality read ends and for counting methylation level.

::DEVELOPER

Algorithms and Computational Biology Lab ,University of California / Bayesian Statistics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 BRAT

:: MORE INFORMATION

Citation:

Harris EY, Ounit R, Lonardi S.
BRAT-nova: fast and accurate mapping of bisulfite-treated reads.
Bioinformatics. 2016 Sep 1;32(17):2696-8. doi: 10.1093/bioinformatics/btw226. Epub 2016 Apr 23. PMID: 27153660.

Bioinformatics. 2012 Jul 1;28(13):1795-6. doi: 10.1093/bioinformatics/bts264. Epub 2012 May 3.
BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.
Harris EY1, Ponts N, Le Roch KG, Lonardi S.

Marttinen, Pekka, Adam Baldwin, William P. Hanage, Chris Dowson, Esh Mahenthiralingam and Corander, Jukka, 2008,
Bayesian Modeling of Recombination Events in Bacterial Populations,
BMC Bioinformatics 9:421.

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