name: megahit-assembler description: MEGAHIT metagenomic assembly skill for reconstructing genomes from short reads allowed-tools:
- Read
- Write
- Glob
- Grep
- Edit
- WebFetch
- WebSearch
- Bash
metadata:
version: "1.0"
category: bioinformatics
tags:
- metagenomics
- assembly
- genomes
- contigs
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)