megahit-assembler
// MEGAHIT metagenomic assembly skill for reconstructing genomes from short reads
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updated:March 4, 2026
SKILL.mdreadonly
SKILL.md Frontmatter
namemegahit-assembler
descriptionMEGAHIT metagenomic assembly skill for reconstructing genomes from short reads
allowed-toolsRead,Write,Glob,Grep,Edit,WebFetch,WebSearch,Bash
metadata[object Object]
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)