Agent
atacseq-pipeline
Execute ENCODE ATAC-seq pipeline from FASTQ to accessibility peaks with Tn5 correction, Bowtie2, and MACS2
@ammawlaView AgentData
Agent
wgbs-pipeline
Execute ENCODE WGBS pipeline from FASTQ to methylation calls using Bismark and MethylDackel
Install
> /plugin marketplace add ammawla/encode-toolkit > /plugin install encode-toolkit@ammawla
How it fires
How this agent gets triggered: by you, by Claude, or both.
- Fires itselfAuto-invocation. Claude auto-loads it when your prompt matches the work.Auto-invocation is when the right skill fires by itself at the right moment, driven by a FLOW.md router and a hook, instead of you invoking it by name. It is the difference between a skill being installed and a skill actually getting used.Read the full definition →
- You can call itInvoke it directly when you want it.
Context preview
The summary Claude sees to decide when to auto-load this agent.
Execute ENCODE WGBS pipeline from FASTQ to methylation calls using Bismark and MethylDackel
Agent definition
wgbs-pipeline.mdname: wgbs-pipeline description: Execute ENCODE WGBS pipeline from FASTQ to methylation calls using Bismark and MethylDackel
WGBS Pipeline Agent
You are an ENCODE Whole Genome Bisulfite Sequencing specialist. Guide users through the complete pipeline:
Pipeline Stages
1. **QC & Trimming**: FastQC + Trim Galore (adapter + RRBS mode if applicable) 2. **Alignment**: Bismark (Bowtie2 backend) to bisulfite-converted GRCh38/mm10 3. **Deduplication**: Bismark deduplicate for PCR duplicate removal 4. **Methylation Extraction**: MethylDackel for per-CpG methylation levels 5. **QC Metrics**: Conversion rate from lambda/pUC19 spike-in, coverage statistics
Quality Thresholds
- Bisulfite conversion rate >= 98%
- CpG coverage >= 10x for DMR calling
- Lambda/pUC19 spike-in for conversion QC
Output Types
- bedMethyl: Per-CpG methylation levels (chr, start, end, methylation%, coverage)
- bigBed: Browser-compatible methylation tracks
- HMR/UMR/PMD regions (if called)
Tools
Use `encode_search_experiments` with assay_title="WGBS" to find data.
Refer to the pipeline-wgbs skill for full Nextflow implementation.
Ships withencode-toolkit
Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.
Get the whole plugin
Stats
24
Stars
5
Forks
Maintained
Maintenance
Python
Language
AGPL-3.0
License
1mo ago
Last commit
6mo ago
Created
Repo: ammawla/encode-toolkit
Other agents on encode-toolkit.
@ammawlaView AgentAgent
chipseq-pipeline
Execute ENCODE ChIP-seq pipeline from FASTQ to peaks and signal tracks using BWA-MEM, MACS2, and IDR
@ammawlaView AgentAgent
cutandrun-pipeline
Execute CUT&RUN pipeline from FASTQ to peaks with Bowtie2, SEACR, and spike-in normalization
@ammawlaView AgentAgent
dnaseseq-pipeline
Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints using BWA, Hotspot2, and HINT-ATAC
@ammawlaView AgentAgent
hic-pipeline
Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls using BWA, pairtools, Juicer, and HiCCUPS
@ammawlaView AgentAgent
rnaseq-pipeline
Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification using STAR 2-pass alignment and RSEM/Kallisto
@ammawlaView Agent