megahit-assembler

# 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)