Page updated 01/03/2016
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
Please read User Manual BRAT-nova
Please read User Manual BRAT-bw
Please read User Manual BRAT
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)
Elena Harris <elenah@cs.ucr.edu>