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

页数：11

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