BRAT: bisulfite-treated reads analysis tool.
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ABSTRACT: 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.
SUBMITTER: Harris EY
PROVIDER: S-EPMC3716225 | biostudies-literature | 2010 Feb
REPOSITORIES: biostudies-literature
Publications
BRAT: bisulfite-treated reads analysis tool.
Harris Elena Y EY Ponts Nadia N Levchuk Aleksandr A Roch Karine Le KL Lonardi Stefano S
Bioinformatics (Oxford, England) 20091222 4
<h4>Summary</h4>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 coun ...[more]
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