# Best Practice Pipelines ## 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](https://github.com/EpiDiverse/snps) 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. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://epidiverse.gitbook.io/project/-MfxkdBDZggX_vc_sG5l/epidiverse-pipelines/best-practice-pipelines.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.