Customizable workflows based on snakemake and python for the analysis of NGS data

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

Arioc: GPU-accelerated DNA short-read alignment

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

Pipelines in genomics

BiSulfite Bolt - A Bisulfite Sequencing Alignment and Processing Tool

Suite of tools to conduct methylation data analysis. Methods from this workspace can be used for alignment and quality control analysis for various protocols including Whole Genom Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS) and Hybrid Selection Bisulfite Sequencing (HSBS).

Differential methylation: Easy, Fast, Identification and ANnoTation

Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

Targeted Amplicon Bisulfite Sequencing Analysis Tool

bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatics pipeline able to perform a full DNA methylation level analysis

a SGE, python, implementation of the ENCODE consortium whole genome bisulfite sequencing pipeline.

Pipeline for BS-Seq data based on snakemake

A SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids.

Bisulfite Sequencing Virus integration Finder

A simple python script to find the amount of methylation after bisulfites sequencing from .fasta files

bisulfite sequencing pattern analysis tool

A Bioconductor ExperimentHub data package for flow sorted purified whole blood cell types measured using DNA methylation on WGBS platform from BLUEPRINT

Analyze Whole Genome Bi-Sulfite Sequencing for Grape evolution in response to grafting

PARamrfinder is a high performance parallel tool to predict allele-specific DNA methylation (ASM) in mammals in the absence of SNP data.