Elena Y Harris1, Rachid Ounit2, Stefano Lonardi2. 1. Department of Computer Science, California State University, Chico, CA 95929, USA. 2. Department of Computer Science and Eng, University of California, Riverside, CA 92521, USA.
Abstract
UNLABELLED: In response to increasing amounts of sequencing data, faster and faster aligners need to become available. Here, we introduce BRAT-nova, a completely rewritten and improved implementation of the mapping tool BRAT-BW for bisulfite-treated reads (BS-Seq). BRAT-nova is very fast and accurate. On the human genome, BRAT-nova is 2-7 times faster than state-of-the-art aligners, while maintaining the same percentage of uniquely mapped reads and space usage. On synthetic reads, BRAT-nova is 2-8 times faster than state-of-the-art aligners while maintaining similar mapping accuracy, methylation call accuracy, methylation level accuracy and space efficiency. AVAILABILITY AND IMPLEMENTATION: The software is available in the public domain at http://compbio.cs.ucr.edu/brat/ CONTACT: elenah@cs.ucr.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
UNLABELLED: In response to increasing amounts of sequencing data, faster and faster aligners need to become available. Here, we introduce BRAT-nova, a completely rewritten and improved implementation of the mapping tool BRAT-BW for bisulfite-treated reads (BS-Seq). BRAT-nova is very fast and accurate. On the human genome, BRAT-nova is 2-7 times faster than state-of-the-art aligners, while maintaining the same percentage of uniquely mapped reads and space usage. On synthetic reads, BRAT-nova is 2-8 times faster than state-of-the-art aligners while maintaining similar mapping accuracy, methylation call accuracy, methylation level accuracy and space efficiency. AVAILABILITY AND IMPLEMENTATION: The software is available in the public domain at http://compbio.cs.ucr.edu/brat/ CONTACT: elenah@cs.ucr.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.