Lars Bolund

BS-SNPer: SNP calling in Bisulfite-seq data

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Standard

BS-SNPer : SNP calling in Bisulfite-seq data. / Gao, Shengjie; Zou, Dan; Mao, Likai; Liu, Huayu; Song, Pengfei; Chen, Youguo; Zhao, Shancen; Gao, Changduo; Li, Xiangchun; Gao, Zhibo; Fang, Xiaodong; Yang, Huanming; Ørntoft, Torben F; Sørensen, Karina D; Bolund, Lars.

I: Bioinformatics (Online), Bind 31, 28.08.2015.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Harvard

Gao, S, Zou, D, Mao, L, Liu, H, Song, P, Chen, Y, Zhao, S, Gao, C, Li, X, Gao, Z, Fang, X, Yang, H, Ørntoft, TF, Sørensen, KD & Bolund, L 2015, 'BS-SNPer: SNP calling in Bisulfite-seq data', Bioinformatics (Online), bind 31. https://doi.org/10.1093/bioinformatics/btv507

APA

Gao, S., Zou, D., Mao, L., Liu, H., Song, P., Chen, Y., Zhao, S., Gao, C., Li, X., Gao, Z., Fang, X., Yang, H., Ørntoft, T. F., Sørensen, K. D., & Bolund, L. (2015). BS-SNPer: SNP calling in Bisulfite-seq data. Bioinformatics (Online), 31. https://doi.org/10.1093/bioinformatics/btv507

CBE

Gao S, Zou D, Mao L, Liu H, Song P, Chen Y, Zhao S, Gao C, Li X, Gao Z, Fang X, Yang H, Ørntoft TF, Sørensen KD, Bolund L. 2015. BS-SNPer: SNP calling in Bisulfite-seq data. Bioinformatics (Online). 31. https://doi.org/10.1093/bioinformatics/btv507

MLA

Vancouver

Gao S, Zou D, Mao L, Liu H, Song P, Chen Y o.a. BS-SNPer: SNP calling in Bisulfite-seq data. Bioinformatics (Online). 2015 aug 28;31. https://doi.org/10.1093/bioinformatics/btv507

Author

Gao, Shengjie ; Zou, Dan ; Mao, Likai ; Liu, Huayu ; Song, Pengfei ; Chen, Youguo ; Zhao, Shancen ; Gao, Changduo ; Li, Xiangchun ; Gao, Zhibo ; Fang, Xiaodong ; Yang, Huanming ; Ørntoft, Torben F ; Sørensen, Karina D ; Bolund, Lars. / BS-SNPer : SNP calling in Bisulfite-seq data. I: Bioinformatics (Online). 2015 ; Bind 31.

Bibtex

@article{944ac4c1e423465abb0947e3f7641dc2,
title = "BS-SNPer: SNP calling in Bisulfite-seq data",
abstract = "Sodium bisulfite conversion followed by sequencing (BS-Seq, such as whole genome bisulfite sequencing or reduced representation bisulfite sequencing) has become popular for studying human epigenetic profiles. Identifying single nucleotide polymorphisms (SNPs) is important for quantification of methylation levels and for study of allele-specific epigenetic events such as imprinting. However, SNP calling in such data is complex and time consuming. Here we present an ultrafast and memory-efficient package named BS-SNPer for the exploration of SNP sites from BS-Seq data. Compared to Bis-SNP, a popular BS-Seq specific SNP caller, BS-SNPer is over 100 times faster and uses less memory. BS-SNPer also offers higher sensitivity and specificity compared to existing methods.AVAILABILITY AND IMPLEMENTATION: BS-SNPer is written in C++ and Perl, and is freely available at https://github.com/hellbelly/BS-Snper.CONTACT: bolund@biomed.au.dk, kdso@clin.au.dk or orntoft@ki.au.dk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",
author = "Shengjie Gao and Dan Zou and Likai Mao and Huayu Liu and Pengfei Song and Youguo Chen and Shancen Zhao and Changduo Gao and Xiangchun Li and Zhibo Gao and Xiaodong Fang and Huanming Yang and {\O}rntoft, {Torben F} and S{\o}rensen, {Karina D} and Lars Bolund",
note = "{\textcopyright} The Author(s) 2015. Published by Oxford University Press.",
year = "2015",
month = aug,
day = "28",
doi = "10.1093/bioinformatics/btv507",
language = "English",
volume = "31",
journal = "Bioinformatics (Online)",
issn = "1367-4811",
publisher = "Oxford University Press",

}

RIS

TY - JOUR

T1 - BS-SNPer

T2 - SNP calling in Bisulfite-seq data

AU - Gao, Shengjie

AU - Zou, Dan

AU - Mao, Likai

AU - Liu, Huayu

AU - Song, Pengfei

AU - Chen, Youguo

AU - Zhao, Shancen

AU - Gao, Changduo

AU - Li, Xiangchun

AU - Gao, Zhibo

AU - Fang, Xiaodong

AU - Yang, Huanming

AU - Ørntoft, Torben F

AU - Sørensen, Karina D

AU - Bolund, Lars

N1 - © The Author(s) 2015. Published by Oxford University Press.

PY - 2015/8/28

Y1 - 2015/8/28

N2 - Sodium bisulfite conversion followed by sequencing (BS-Seq, such as whole genome bisulfite sequencing or reduced representation bisulfite sequencing) has become popular for studying human epigenetic profiles. Identifying single nucleotide polymorphisms (SNPs) is important for quantification of methylation levels and for study of allele-specific epigenetic events such as imprinting. However, SNP calling in such data is complex and time consuming. Here we present an ultrafast and memory-efficient package named BS-SNPer for the exploration of SNP sites from BS-Seq data. Compared to Bis-SNP, a popular BS-Seq specific SNP caller, BS-SNPer is over 100 times faster and uses less memory. BS-SNPer also offers higher sensitivity and specificity compared to existing methods.AVAILABILITY AND IMPLEMENTATION: BS-SNPer is written in C++ and Perl, and is freely available at https://github.com/hellbelly/BS-Snper.CONTACT: bolund@biomed.au.dk, kdso@clin.au.dk or orntoft@ki.au.dk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - Sodium bisulfite conversion followed by sequencing (BS-Seq, such as whole genome bisulfite sequencing or reduced representation bisulfite sequencing) has become popular for studying human epigenetic profiles. Identifying single nucleotide polymorphisms (SNPs) is important for quantification of methylation levels and for study of allele-specific epigenetic events such as imprinting. However, SNP calling in such data is complex and time consuming. Here we present an ultrafast and memory-efficient package named BS-SNPer for the exploration of SNP sites from BS-Seq data. Compared to Bis-SNP, a popular BS-Seq specific SNP caller, BS-SNPer is over 100 times faster and uses less memory. BS-SNPer also offers higher sensitivity and specificity compared to existing methods.AVAILABILITY AND IMPLEMENTATION: BS-SNPer is written in C++ and Perl, and is freely available at https://github.com/hellbelly/BS-Snper.CONTACT: bolund@biomed.au.dk, kdso@clin.au.dk or orntoft@ki.au.dk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

U2 - 10.1093/bioinformatics/btv507

DO - 10.1093/bioinformatics/btv507

M3 - Journal article

C2 - 26319221

VL - 31

JO - Bioinformatics (Online)

JF - Bioinformatics (Online)

SN - 1367-4811

ER -