epiGBSBS: reference-free reduced representation bisulfite sequencing

T. van Gurp; C.A.M. Wagemaker; B. Wouters; P. Vergeer; N.J. Ouborg; Koen J.F.  Verhoeven

doi:10.1038/nmeth.3763

epiGBSBS: reference-free reduced representation bisulfite sequencing

T. van Gurp^*, C.A.M. Wagemaker, B. Wouters, P. Vergeer, N.J. Ouborg, Koen J.F. Verhoeven^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

94 Citations (Scopus)

Abstract

We describe epiGBSBS, a reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNADNADNA methylation and genetic variation in hundreds of samples de novo. This method uses genotyping by sequencing of bisulfite-converted DNADNADNA followed by reliable de novo reference construction, mapping, variant calling, and distinction of single-nucleotide polymorphisms (SNSNPs) versus methylation variation (software is available at https://github.com/thomasvangurp/epiGBS). The output can be loaded directly into a genome browser for visualization and into RnBeads for analysis of differential methylation.

Original language	English
Pages (from-to)	322-324
Journal	Nature Methods : techniques for life scientists and chemists
Volume	13
DOIs	https://doi.org/10.1038/nmeth.3763
Publication status	Published - 2016

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abstract = "We describe epiGBSBS, a reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNADNADNA methylation and genetic variation in hundreds of samples de novo. This method uses genotyping by sequencing of bisulfite-converted DNADNADNA followed by reliable de novo reference construction, mapping, variant calling, and distinction of single-nucleotide polymorphisms (SNSNPs) versus methylation variation (software is available at https://github.com/thomasvangurp/epiGBS). The output can be loaded directly into a genome browser for visualization and into RnBeads for analysis of differential methylation.",

author = "{van Gurp}, T. and C.A.M. Wagemaker and B. Wouters and P. Vergeer and N.J. Ouborg and Verhoeven, {Koen J.F.}",

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AU - van Gurp, T.

AU - Wagemaker, C.A.M.

AU - Wouters, B.

AU - Vergeer, P.

AU - Ouborg, N.J.

AU - Verhoeven, Koen J.F.

PY - 2016

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AB - We describe epiGBSBS, a reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNADNADNA methylation and genetic variation in hundreds of samples de novo. This method uses genotyping by sequencing of bisulfite-converted DNADNADNA followed by reliable de novo reference construction, mapping, variant calling, and distinction of single-nucleotide polymorphisms (SNSNPs) versus methylation variation (software is available at https://github.com/thomasvangurp/epiGBS). The output can be loaded directly into a genome browser for visualization and into RnBeads for analysis of differential methylation.

U2 - 10.1038/nmeth.3763

DO - 10.1038/nmeth.3763

M3 - Article

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JO - Nature Methods : techniques for life scientists and chemists

JF - Nature Methods : techniques for life scientists and chemists

ER -

epiGBSBS: reference-free reduced representation bisulfite sequencing

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