epiGBS: reference-free reduced representation bisulfite sequencing: brief communication

TY - JOUR

T1 - epiGBS: reference-free reduced representation bisulfite sequencing

T2 - brief communication

AU - van Gurp, Thomas P

AU - Wagemaker, Niels CAM

AU - Wouters, Björn

AU - Vergeer, Philippine

AU - Ouborg, Joop NJ

AU - Verhoeven, Koen JF

N1 - 6038, TE; Data Archiving: Data archived at NCBI

PY - 2016

Y1 - 2016

N2 - We describe epiGBS, a reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNA methylation and genetic variation in hundreds of samples de novo. This method uses genotyping by sequencing of bisulfite-converted DNA followed by reliable de novo reference construction, mapping, variant calling, and distinction of single-nucleotide polymorphisms (SNPs) 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.

AB - We describe epiGBS, a reduced representation bisulfite sequencing method for cost-effective exploration and comparative analysis of DNA methylation and genetic variation in hundreds of samples de novo. This method uses genotyping by sequencing of bisulfite-converted DNA followed by reliable de novo reference construction, mapping, variant calling, and distinction of single-nucleotide polymorphisms (SNPs) 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.

KW - national

UR - http://www.ncbi.nlm.nih.gov/bioproject/PRJNA287755/

U2 - 10.1038/nmeth.3763

DO - 10.1038/nmeth.3763

M3 - Article

SN - 1548-7091

VL - 13

SP - 322

EP - 324

JO - Nature Methods

JF - Nature Methods

IS - 4

ER -