Best Practice Pipelines
The principle analysis software of the EpiDiverse Toolkit
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.
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.
Best practice pipeline for calling differentially methylated regions (DMRs) or positions (DMPs) in pairwise comparisons between groups of samples.
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
A snakemake pipeline for genotyping-by-sequencing using a specialised reduced representation sequencing protocol.
Identification of differentially methylated regions between multiple epigenomes from BS-treated read mappings via methylated region calling.