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claude-codescience

Babysitter megahit-assembler

MEGAHIT metagenomic assembly skill for reconstructing genomes from short reads

install
source · Clone the upstream repo
git clone https://github.com/a5c-ai/babysitter
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/a5c-ai/babysitter "$T" && mkdir -p ~/.claude/skills && cp -r "$T/library/specializations/domains/science/bioinformatics/skills/megahit-assembler" ~/.claude/skills/a5c-ai-babysitter-megahit-assembler && rm -rf "$T"
manifest: library/specializations/domains/science/bioinformatics/skills/megahit-assembler/SKILL.md
tags
#metagenomics#assembly#genomes#contigs#k-mer#binning
source content

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)