BatAlign: an Incremental Method for Accurate Alignment of Sequencing Reads

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2015 Jul 15

PMID 26170239

Citations 5

Authors

Jing-Quan Lim

Chandana Tennakoon

Peiyong Guan

Wing-Kin Sung

Affiliations

Soon will be listed here.

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.

Citing Articles

Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals.

Gong W, Pan X, Xu D, Ji G, Wang Y, Tian Y Comput Struct Biotechnol J. 2022; 20:4704-4716.

PMID: 36147684 PMC: 9465269. DOI: 10.1016/j.csbj.2022.08.051.

An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping.

Zhou Q, Lim J, Sung W, Li G BMC Bioinformatics. 2019; 20(1):47.

PMID: 30669962 PMC: 6343306. DOI: 10.1186/s12859-018-2593-4.

Performance evaluation method for read mapping tool in clinical panel sequencing.

Lee H, Lee K, Lee T, Park D, Chung J, Lee C Genes Genomics. 2018; 40(2):189-197.

PMID: 29568413 PMC: 5846869. DOI: 10.1007/s13258-017-0621-9.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

Zheng Q, Grice E PLoS Comput Biol. 2016; 12(10):e1005096.

PMID: 27706155 PMC: 5051939. DOI: 10.1371/journal.pcbi.1005096.

Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data.

Kofler R, Langmuller A, Nouhaud P, Otte K, Schlotterer C G3 (Bethesda). 2016; 6(11):3507-3515.

PMID: 27613752 PMC: 5100849. DOI: 10.1534/g3.116.034488.

References

Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S . Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. PMC: 545600. DOI: 10.1186/gb-2004-5-10-r80. View

Ma B, Tromp J, Li M . PatternHunter: faster and more sensitive homology search. Bioinformatics. 2002; 18(3):440-5. DOI: 10.1093/bioinformatics/18.3.440. View

Li R, Li Y, Kristiansen K, Wang J . SOAP: short oligonucleotide alignment program. Bioinformatics. 2008; 24(5):713-4. DOI: 10.1093/bioinformatics/btn025. View

Farrar M . Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics. 2006; 23(2):156-61. DOI: 10.1093/bioinformatics/btl582. View

Mills R, Luttig C, Larkins C, Beauchamp A, Tsui C, Pittard W . An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 2006; 16(9):1182-90. PMC: 1557762. DOI: 10.1101/gr.4565806. View

Smith A, Xuan Z, Zhang M . Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics. 2008; 9:128. PMC: 2335322. DOI: 10.1186/1471-2105-9-128. View

Lin H, Zhang Z, Zhang M, Ma B, Li M . ZOOM! Zillions of oligos mapped. Bioinformatics. 2008; 24(21):2431-7. PMC: 2732274. DOI: 10.1093/bioinformatics/btn416. View

Li H, Ruan J, Durbin R . Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008; 18(11):1851-8. PMC: 2577856. DOI: 10.1101/gr.078212.108. View

Rumble S, Lacroute P, Dalca A, Fiume M, Sidow A, Brudno M . SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol. 2009; 5(5):e1000386. PMC: 2678294. DOI: 10.1371/journal.pcbi.1000386. View

10.

Langmead B, Trapnell C, Pop M, Salzberg S . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):R25. PMC: 2690996. DOI: 10.1186/gb-2009-10-3-r25. View

11.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

12.

Chen K, Wallis J, McLellan M, Larson D, Kalicki J, Pohl C . BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009; 6(9):677-81. PMC: 3661775. DOI: 10.1038/nmeth.1363. View

13.

Weese D, Emde A, Rausch T, Doring A, Reinert K . RazerS--fast read mapping with sensitivity control. Genome Res. 2009; 19(9):1646-54. PMC: 2752123. DOI: 10.1101/gr.088823.108. View

14.

Chen Y, Souaiaia T, Chen T . PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics. 2009; 25(19):2514-21. PMC: 2752623. DOI: 10.1093/bioinformatics/btp486. View

15.

Degner J, Marioni J, Pai A, Pickrell J, Nkadori E, Gilad Y . Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics. 2009; 25(24):3207-12. PMC: 2788925. DOI: 10.1093/bioinformatics/btp579. View

16.

Yang H, Zhong Y, Peng C, Chen J, Tian D . Important role of indels in somatic mutations of human cancer genes. BMC Med Genet. 2010; 11:128. PMC: 2940769. DOI: 10.1186/1471-2350-11-128. View

17.

Abecasis G, Altshuler D, Auton A, Brooks L, Durbin R, Gibbs R . A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061-73. PMC: 3042601. DOI: 10.1038/nature09534. View

18.

Lunter G, Goodson M . Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 2010; 21(6):936-9. PMC: 3106326. DOI: 10.1101/gr.111120.110. View

19.

Danecek P, Auton A, Abecasis G, Albers C, Banks E, DePristo M . The variant call format and VCFtools. Bioinformatics. 2011; 27(15):2156-8. PMC: 3137218. DOI: 10.1093/bioinformatics/btr330. View

20.

Wang J, Mullighan C, Easton J, Roberts S, Heatley S, Ma J . CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods. 2011; 8(8):652-4. PMC: 3527068. DOI: 10.1038/nmeth.1628. View