title: BatAlign: an incremental method for accurate alignment of sequencing reads.
abstract: Structural variations (SVs) play a crucial role in genetic diversity. However, the alignments of reads near/across SVs are made inaccurate by the presence of polymorphisms. BatAlign is an algorithm that integrated two strategies called 'Reverse-Alignment' and 'Deep-Scan' to improve the accuracy of read-alignment. In our experiments, BatAlign was able to obtain the highest F-measures in read-alignments on mismatch-aberrant, indel-aberrant, concordantly/discordantly paired and SV-spanning data sets. On real data, the alignments of BatAlign were able to recover 4.3% more PCR-validated SVs with 73.3% less callings. These suggest BatAlign to be effective in detecting SVs and other polymorphic-variants accurately using high-throughput data. BatAlign is publicly available at https://goo.gl/a6phxB.
authors.affiliation: Department of Computer Science, National University of Singapore, Singapore 117417 Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169610.
authors.forename: Jing-Quan
authors.initials: JQ
authors.lastname: Lim
authors.affiliation: Department of Computer Science, National University of Singapore, Singapore 117417 NUS Graduate School for Integrative Sciences and Engineering, (CeLS), #05-01, 28 Medical Drive, Singapore 117456 Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672 UAE University, PO Box 17551, Al Ain, UAE.
authors.forename: Chandana
authors.initials: C
authors.lastname: Tennakoon
authors.affiliation: Department of Computer Science, National University of Singapore, Singapore 117417.
authors.forename: Peiyong
authors.initials: P
authors.lastname: Guan
authors.affiliation: Department of Computer Science, National University of Singapore, Singapore 117417 Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672 ksung@comp.nus.edu.sg.
authors.forename: Wing-Kin
authors.initials: WK
authors.lastname: Sung
mesh_terms: D000465:Algorithms; D020137:Base Pair Mismatch; D016678:Genome; D056914:Genomic Structural Variation; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D016415:Sequence Alignment / Q000379:methods*