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genomeassembler

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Run genome assemblies without guesswork.

Education & Research#scaffolding#bioinformatics#nf-core#nextflow#polishing#genome assembly#long reads
Authordanilomonge
Version1.0.0
Installs0

System Documentation

What problem does it solve?

nf-core/genomeassembler is powerful but complex, with many interdependent options, release-specific behaviors, and strict input requirements. This Skill turns that complexity into a reliable guided workflow so you can launch genome assembly runs without guessing flags or parameter values.

Core Features & Use Cases

  • Long-read genome assembly: Supports assembly workflows for ONT and PacBio HiFi datasets.
  • Polishing and scaffolding: Helps choose and configure polishing with Medaka or Pilon, and scaffolding with LINKS, Longstitch, or RagTag when applicable.
  • Validated execution: Uses the correct samplesheet structure, required inputs, and release-pinned configuration for reproducible runs.
  • Practical use cases: Ideal for starting a new assembly, rerunning a specific pipeline release, or preparing a safe demo execution with the right profile and inputs.

Quick Start

Ask the assistant to run the genomeassembler skill on your samplesheet and output directory, then select the needed profile and optional parameters from the skill reference.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: genomeassembler
Download link: https://github.com/danilomonge/nf-claw/archive/main.zip#genomeassembler

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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