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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 graph: domains: [domain:bioinformatics] specializations: [specialization:biomedical-informatics] skillAreas: [skill-area:graph-algorithms, skill-area:python-data-pipelines, skill-area:data-analysis] workflows: [workflow:experiment-design] roles: [role:research-engineer, role:biomedical-engineer]

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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)