Best Practice Pipelines

https://github.com/EpiDiverse/wgbs

Best practice pipeline for processing and aligning whole genome bisulfite sequencing (WGBS) data from non-model plant species, ready for downstream analysis with the other following EpiDiverse pipelines.

https://github.com/EpiDiverse/snp

Best practice pipeline for calling single nucleotide polymorphism (SNP) variants from bisulfite sequencing data and/or for clustering of eg. environmental samples according to methylation profiles while masking genomic variation.

https://github.com/EpiDiverse/dmr

Best practice pipeline for calling differentially methylated regions (DMRs) or positions (DMPs) in pairwise comparisons between groups of samples.

https://github.com/EpiDiverse/ewas

Best practice pipeline for epigenome-wide association studies (EWAS) from individual sample methylation calls which are optionally filtered according to DMRs or DMPs.

Recommended External Pipelines

https://github.com/nioo-knaw/epiGBS2

A snakemake pipeline for genotyping-by-sequencing using a specialised reduced representation sequencing protocol.

https://github.com/Computomics/MethylScore

Identification of differentially methylated regions between multiple epigenomes from BS-treated read mappings via methylated region calling.