epiGBS specifications

Information


Unique identifier OMICS_13278
Name epiGBS
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
PEAR, usearch, seqtk, pysam, bioPython, bcftools, samtools, vcfutils.pl, pyfaidx, rename_fast.py, pigz, bwa-mem
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Thomas P. van Gurp

Publication for epiGBS

epiGBS citations

 (2)
library_books

Notos a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types

2018
BMC Bioinformatics
PMCID: 5870242
PMID: 29587630
DOI: 10.1186/s12859-018-2115-4

[…] igestion method are methylation sensitive amplified length polymorphism (MS-AFLP) [], reduced-restriction bisulfite sequencing (RRBS) [] or reference-free reduced representation bisulfite sequencing (epiGBS) []. These methods are very powerful and can be used with or without a reference genome (that is not necessarily available for non-model species). A caveat of RRBS is however that it was design […]

library_books

Plant RRBS, a bisulfite and next generation sequencing based methylome profiling method enriching for coverage of cytosine positions

2017
BMC Plant Biol
PMCID: 5501559
PMID: 28683715
DOI: 10.1186/s12870-017-1070-y

[…] mportant role in polyploid genome evolution [] and at Quercus gene promoters in response to temperature regimes []. Methylation detection was combined with GBS (genotyping by sequencing) resulting in epiGBS, applicable also to non-model plant species lacking a reference genome, allowing to detect methylation polymorphisms from bisulfite-converted samples, but with the need to reconstruct the conse […]

epiGBS institution(s)
Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands; Department of Experimental Plant Ecology, Radboud University, Nijmegen, Netherlands; Plant Ecology and Nature Conservation Group, Wageningen University, Wageningen, Netherlands
epiGBS funding source(s)
This study was funded by the Netherlands Organization for Scientific Research (NWO-ALW grants 864.10.008 and 820.01.025).

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