Journal Article

BRAT: bisulfite-treated reads analysis tool

Elena Y. Harris, Nadia Ponts, Aleksandr Levchuk, Karine Le Roch and Stefano Lonardi

in Bioinformatics

Volume 26, issue 4, pages 572-573
Published in print February 2010 | ISSN: 1367-4803
Published online December 2009 | e-ISSN: 1460-2059 | DOI:
BRAT: bisulfite-treated reads analysis tool

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Summary: We present a new, accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Our tool, BRAT, supports single and paired-end reads and handles input files containing reads and mates of different lengths. BRAT is faster, maps more unique paired-end reads and has higher accuracy than existing programs. The software package includes tools to end-trim low-quality bases of the reads and to report nucleotide counts for mapped reads on the reference genome.

Availability: The source code is freely available for download at and is distributed as Open Source software under the GPLv3.0.


Journal Article.  1616 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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