Process WGBS FASTQ files into ENCODE-compliant methylation calls.
npx skills add https://github.com/ammawla/encode-toolkit --skill pipeline-wgbs
Please help me install this Agent Skill. Skill: pipeline-wgbs Source: https://github.com/ammawla/encode-toolkit/tree/main/plugin/skills/pipeline-wgbs Command: npx skills add https://github.com/ammawla/encode-toolkit --skill pipeline-wgbs
This Skill enables users to process and analyze whole-genome bisulfite sequencing data for comprehensive methylation profiling, ensuring high-quality, standardized results.
Run the WGBS pipeline on your FASTQ files with a command specifying input files and reference genome to obtain methylation calls compatible with ENCODE standards.
High-intent search queries and answers about installing and using this skill.
To process raw WGBS FASTQ files, you perform adapter trimming, bisulfite-aware alignment, deduplication, and methylation extraction to generate high-confidence calls. This pipeline handles these steps end-to-end to produce bedMethyl files for downstream epigenomic analysis.
Whole-genome bisulfite sequencing quality control requires evaluating bisulfite conversion rates, coverage, mapping, and duplication metrics. This pipeline ensures these metrics meet ENCODE standards, providing standardized QC reports through MultiQC for reliable epigenomic research.
Yes, this methylation analysis pipeline supports Bismark for bisulfite-aware alignment. It integrates Bismark alongside BWA, Trim Galore, and Picard to execute the core processing steps required for comprehensive whole-genome bisulfite sequencing analysis.
The best way to ensure WGBS methylation calls adhere to ENCODE standards is by using a standardized processing pipeline with built-in QC metrics. This approach validates bisulfite conversion rates and alignment quality to guarantee high-confidence epigenomic results.
Yes, you can use Nextflow to automate end-to-end WGBS data processing. This pipeline leverages Nextflow to orchestrate the entire workflow, from adapter trimming and bisulfite-aware alignment to methylation extraction and quality assessment.
ya-wayProcess bisulfite sequencing FASTQ data into differentially methylated regions.
inflexa-aiAnalyze DNA methylation data from Illumina arrays and bisulfite sequencing.
MubasherMohammedAggregate bioinformatics QC reports into MultiQC HTML and ClawBio markdown summaries.
Victory-HugoRead, write, and analyze SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ genomic data via Python.
