BRAT-nova: fast and accurate mapping of bisulfite-treated reads

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 hu...

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2016-09, Vol.32 (17), p.2696-2698
Main Authors: Harris, Elena Y, Ounit, Rachid, Lonardi, Stefano
Format: Article
Language:English
Subjects:
Chromosome Mapping
DNA Methylation
Genome, Human
High-Throughput Nucleotide Sequencing
Humans
Sequence Alignment
Sequence Analysis, DNA
Software
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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. The software is available in the public domain at http://compbio.cs.ucr.edu/brat/ elenah@cs.ucr.edu Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btw226