longraredisease

Run the nf-core/longraredisease pipeline from a validated samplesheet and reference genome.

1|Updated Jun 19, 2026

Search Tags:#bioinformatics #nf-core #nextflow #rare disease #variant-calling #long-read sequencing

Ready to run

npx skills add https://github.com/danilomonge/nf-claw --skill longraredisease

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: longraredisease
Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/longraredisease
Command: npx skills add https://github.com/danilomonge/nf-claw --skill longraredisease

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

nf-core/longraredisease removes the manual effort of configuring a complex rare-disease sequencing workflow by packaging the pipeline, its parameters, and its run instructions into one dependable skill.

Core Features & Use Cases

Long-read variant analysis: Run SNV, SV, CNV, STR, and methylation workflows for Oxford Nanopore or PacBio data.
Clinical-style guardrails: Use schema-validated inputs, pinned releases, and documented outputs to avoid invalid runs and guesswork.
Reproducible execution: Keep provenance, parameter constraints, and pipeline documentation aligned so results are easier to review and repeat.

Quick Start

Ask the assistant to run the longraredisease pipeline for your samplesheet and FASTA genome, then save the results in your chosen output directory.

Frequently Asked Questions about longraredisease

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I run rare-disease long-read sequencing analysis for SNV, SV, CNV, STR, and methylation variants?▼

Rare-disease long-read sequencing analysis for SNV, SV, CNV, STR, and methylation variants is run using the nf-core/longraredisease pipeline from a validated samplesheet and reference genome. It supports Oxford Nanopore and PacBio cohorts.

Can I use Oxford Nanopore and PacBio data for long-read variant calling in the same workflow?▼

Yes, long-read variant calling supports both Oxford Nanopore and PacBio data within the same workflow. The pipeline processes these cohort datasets to detect SNV, SV, CNV, STR, and methylation calls.

How do I ensure reproducible execution and provenance capture for rare-disease long-read pipeline runs?▼

Reproducible execution and provenance capture for rare-disease long-read pipeline runs are ensured through schema-constrained parameters, release-pinned execution, and documented outputs. This configuration keeps results easier to review and repeat.

What's the best way to configure Nextflow bioinformatics workflows for rare disease analysis without manual setup?▼

Configuring Nextflow bioinformatics workflows for rare disease analysis without manual setup is handled by packaging the nf-core pipeline, schema-validated parameters, and run instructions together. This removes the effort of manual configuration.

Do I need a validated samplesheet and FASTA genome to start long-read variant analysis?▼

Yes, a validated samplesheet and FASTA reference genome are required to start long-read variant analysis. Schema-validated inputs avoid invalid runs and guesswork by constraining parameters before execution.

What are the limitations of using schema-constrained parameters for long-read rare disease workflows?▼

Schema-constrained parameters for long-read rare disease workflows limit flexibility by enforcing strict input validation and release-pinned execution. This prevents invalid runs but requires inputs to strictly match the expected schema format.