BatAlign: an incremental method for accurate alignment of sequencing reads

被引：8
|
作者：
Lim, Jing-Quan [1 ,2 ]
Tennakoon, Chandana [1 ,3 ,4 ,5 ]
Guan, Peiyong [1 ]
Sung, Wing-Kin [1 ,4 ]
机构：
[1] Natl Univ Singapore, Dept Comp Sci, Singapore 117417, Singapore
[2] Natl Canc Ctr Singapore, Div Med Sci, Lab Canc Epigenome, Singapore 169610, Singapore
[3] NUS Grad Sch Integrat Sci & Engn, CeLS, Singapore 117456, Singapore
[4] Genome Inst Singapore, Dept Computat & Syst Biol, Singapore 138672, Singapore
[5] UAE Univ, Al Ain, U Arab Emirates
来源：
NUCLEIC ACIDS RESEARCH | 2015年 / 43卷 / 16期
关键词：
IDENTIFICATION; ALGORITHM; INSERTION; INDELS; FORMAT;
D O I：
10.1093/nar/gkv533
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
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.
引用
收藏
页数：11
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