brat_bw v2.0.1 (Bisulfite-treated Reads Analysis Tool using 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.
BRAT-bw is BRAT-BW, 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).
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.