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. Availability: The source code is freely available for download at http://compbio.cs.ucr.edu/brat/ and is distributed as Open Source software under the GPLv3.0. Contact: [email protected]

Bioinformatics (2010) 26(4), 572–573 The authors would like to apologize for the erroneous statements on the accuracy of the mapping for mrsFAST (Hormozdiari et al., 2009). The parameters for the insert size used for msrFAST to obtain Figure 1 and Table 1 were not correct; using the correct parameters would have yield higher accuracy than the one reported. At the time of the initial simulation there was no documentation available regarding the distance between the reads for paired-end, so we deduced the definition for the distance from the output files of mrsFAST. For 32 bases paired-end reads (Table 1), we used insert size range from 106 to 306 (called min and max, respectively, in mrsFAST), but the correct values should have been [43, 243]. For 24 bases paired-end reads (Fig. 1), we used [136, 324] whereas the correct values should have been [89, 277]. For 64 bases paired-end reads (Fig. 1), we used [136, 364], but the correct parameters should have been [9, 237].