MEGAHIT Assembler Skill

SkillDev tools

MEGAHIT metagenomic assembly skill for reconstructing genomes from short reads

Instructions available. Your AI can read the instructions. Execution depends on the setup they require.

Account requirements not reviewed. Check the skill instructions before use; ahel provides instructions and does not run this skill.

Add ahel to your AI once: Claude, ChatGPT, Cursor, Claude Code or Codex. Then ask it to use this.

Then ask your AI: use the MEGAHIT Assembler Skill skill

What this skill tells your AI

The instructions your AI receives, as published by a5c-ai/babysitter in library/specializations/domains/science/bioinformatics/skills/megahit-assembler/SKILL.md and read by ahel’s review.

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)

Signals

GitHub stars: 2k
Forks: 112
Last commit: Sep 2026

Advanced

Item type: skill
Key: megahit-assembler
Source: github.com/a5c-ai/babysitter

github.com/a5c-ai/babysitter