Soil Metagenome Pipeline

Soil Metagenome Pipeline is a modular, Nextflow DSL2 workflow for assembling, polishing, binning, annotating, and functionally characterizing complex soil metagenomes. It orchestrates state-of-the-art tools for long- and short-read metagenomics, generates high-quality MAGs, assigns taxonomy, and screens for biosynthetic gene clusters (BGCs).

What it does

• Assembles long-read metagenomes (e.g., ONT) with Flye and optionally polishes with Medaka and/or NextPolish using ...

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