Page updated 01/03/2016

  Bisulfite-treated Reads Analysis Tool


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.

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 is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer. BRAT supports single-end and pair-end short reads mapping and allows alignment of different length reads/mates.

The package includes tools to trim low quality reads ends and to report A, C, G, T counts at each base for forward and reverse strands of references.


Download Link:

downloads (03/01/2016)

To uncompress run:

tar zxvf brat-*.tar.gz

To build:

cd brat-* make

This will create executable programs. Please follow User Manual for instructions about commands and input and output formats.

Please site:
E.Y.Harris, N. Ponts, A. Levchuk, K. Le Roch, S. Lonardi, "BRAT: Bisulfite-treated Reads Analysis Tool", Bioinformatics, December 22, 2009, doi:10.1093/bioinformatics/btp706 .
E.Y.Harris, N. Ponts, K. Le Roch, S. Lonardi, "BRAT-BW: Efficient and accurate mapping of bisulfite-treated reads", Bioinformatics, 2012, doi:10.1093/bioinformatics/bts264

How to Use?

Please read User Manual BRAT-nova

Please read User Manual BRAT-bw

Please read User Manual BRAT

Simulated Test Data

These read data sets were used to benchmark BRAT-nova against BRAT-BW, BS-Seeker2 and Bismark:
Benchmarking data sets for BRAT-nova

The benchmarking scripts together with the command options are provided below:
Benchmarking scripts for BRAT-nova

These in silico generated reads were used to test mapping accuracy and the total number of uniquely mapped reads for mapping tools Bismark, BS-seeker, BRAT, and BRAT-BW. Together with reads, we provide options used with each tool.
Simulated Reads (159MB)

Questions or Comments?

 Elena Harris <>

BRAT is Free and Open Source under GPLv3