Process Hi-C sequencing data into standardized analysis outputs.
npx skills add https://github.com/danilomonge/nf-claw --skill hic
Please help me install this Agent Skill. Skill: hic Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/hic Command: npx skills add https://github.com/danilomonge/nf-claw --skill hic
This Skill streamlines Hi-C sequencing analysis by turning raw chromosome conformation capture data into standardized, reproducible outputs without requiring users to memorize pipeline flags.
Use the hic skill to analyze your Hi-C samplesheet and save the validated results into the output directory you specify.
High-intent search queries and answers about installing and using this skill.
You can generate Hi-C contact maps by providing a validated CSV samplesheet, which triggers paired-end alignment, valid pair detection, and standardized contact map generation without manual pipeline flags.
Yes, the workflow supports both restriction-enzyme digestion and DNase Hi-C protocols, allowing you to process diverse chromosome conformation capture datasets for contact map generation.
To call TADs and compartments from chromosome conformation capture data, run the downstream analysis steps included in the pipeline, with options to skip TAD, compartment, or MultiQC generation as needed.
Reproducible chromosome conformation capture results are enforced through nf-schema parameter validation, required CSV samplesheet inputs, versioned provenance tracking, and standardized output contracts for reliable re-runs.
Yes, you can specify a reference genome or provide custom indices when running the Hi-C pipeline, allowing the workflow to align paired-end reads against your desired reference assembly.
A validated CSV samplesheet is required as the input format for chromosome conformation capture analysis, undergoing nf-schema parameter validation to ensure standardized and reproducible processing outputs.
danilomongeRepair corrupted FASTQ files and restore valid sequencing reads.
zongtingweiIdentify and quantify compartments, loops, and TADs from Hi-C contact matrices.
MubasherMohammedAggregate bioinformatics QC reports into MultiQC HTML and ClawBio markdown summaries.
zerwizRoute genomics and omics tasks to relevant bioinformatics reference skills and pipelines.
