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 short reads.
• Maps short/long reads to assemblies to compute coverage/depth for downstream binning and QC.
• Bins contigs with multiple strategies (SemiBin2, VAMB, MetaCoAG, ComeBIN) and can integrate results.
• Evaluates MAG quality with CheckM2 and assigns taxonomy with GTDB-Tk.
• Annotates bins and/or assemblies (Bakta, eggNOG) and detects BGCs (antiSMASH) with network-based clustering (BiG-SCAPE).
• Produces organized outputs suitable for downstream comparative genomics.

Key features

• Modular DSL2 design: swap/extend modules under modules/ and submodules/.
• Reproducible runtime via Conda/containers (profiles in conf/).
• Sensible defaults with overridable parameters via nextflow.config or CLI.
• Caching and resumability: supports -resume for efficient re-runs.

Modules at a glance (non-exhaustive)

• Assembly and polishing: Flye, Medaka, NextPolish
• Coverage mapping: minimap2/samtools, coverm, strobealign
• Binning: SemiBin2, VAMB, MetaCoAG, ComeBIN, plus bin collection utilities
• QC and taxonomy: CheckM2, GTDB-Tk
• Annotation and function: Bakta (assemblies/bins), eggNOG
• BGC discovery: antiSMASH (assemblies/bins), BiG-SCAPE networks
• Taxonomic profiling: MMseqs2/MetaBuli helpers

Inputs

• Reads: long reads (ONT/PacBio), optional short reads (Illumina).
• Sample sheet: a tab-separated file like data/samples.tsv describing sample IDs and file paths.
• Reference databases: external DBs required by some tools (e.g., GTDB-Tk, antiSMASH, BiG-SCAPE) are not bundled. Configure their locations via params or environment as appropriate.

Quick start

• Dry run / graph preview: nextflow run . -dsl2 -preview

• Example execution (adjust paths and profile to your environment): nextflow run . -profile conda -resume
  --reads '/path/to/_{R1,R2}.fastq.gz'
  --longreads '/path/to/.fastq.gz'
  --samples 'data/samples.tsv'
  --outdir 'results'

See conf/ for example profiles (conda, docker, singularity, slurm). Tune resources via nextflow.config using withName: blocks for process-specific CPU, memory, and time.

Citation

If you use Soil Metagenome Pipeline in your research, please cite the corresponding preprint:

• bioRxiv abstract: https://www.biorxiv.org/content/10.1101/2025.05.28.656579v1.abstract
• DOI: https://doi.org/10.1101/2025.05.28.656579

A machine-readable citation file (CITATION.cff) is included in the repository root. GitHub will display a "Cite this repository" button.

License

This project is licensed under the GNU General Public License v3.0 or later (GPL-3.0-or-later). See the LICENSE file for the full text.