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Megahit assembler

Skill a5c-ai/babysitter/library/specializations/domains/science/bioinformatics/skills/megahit-assembler

MEGAHIT metagenomic assembly skill for reconstructing genomes from short readsFrom its SKILL.md

Install
npx -y skills add a5c-ai/babysitter --skill megahit-assembler

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.3 KB, 152 tokens by cl100k_base, as published. Nobody here has run it

MEGAHIT Assembler Skill

Purpose

Enable MEGAHIT metagenomic assembly for reconstructing genomes from short reads.

Capabilities

  • Memory-efficient assembly
  • Multiple k-mer strategies
  • Contig quality assessment
  • Large dataset handling
  • Iterative assembly refinement
  • Assembly graph analysis

Usage Guidelines

  • Select k-mer strategy based on coverage
  • Assess contig quality metrics
  • Handle large datasets efficiently
  • Consider iterative refinement
  • Bin contigs for MAG recovery
  • Document assembly parameters

Dependencies

  • MEGAHIT
  • metaSPAdes
  • IDBA-UD

Process Integration

  • Shotgun Metagenomics Pipeline (shotgun-metagenomics)

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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