MGnify genomes analysis pipeline

MGnify A pipeline to perform taxonomic and functional annotation and to generate a catalogue from a set of isolate and/or metagenome-assembled genomes (MAGs) using the workflow described in the following publication:

Gurbich TA, Almeida A, Beracochea M, Burdett T, Burgin J, Cochrane G, Raj S, Richardson L, Rogers AB, Sakharova E, Salazar GA and Finn RD. (2023) MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues. J Mol Biol. doi: https://doi.org/10.1016/j.jmb.2023.168016

Detailed information about existing MGnify catalogues: https://docs.mgnify.org/src/docs/genome-viewer.html

Tools used in the pipeline

Setup

Environment

The pipeline is implemented in Nextflow.

Requirements:

• singulairty or docker

Reference databases

The pipeline needs the following reference databases and configuration files (roughtly ~150G):

• ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/genomes-pipeline/gunc_db_2.0.4.dmnd.gz
• ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/genomes-pipeline/eggnog_db.tgz
• ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/genomes-pipeline/rfams_cms/
• ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/genomes-pipeline/kegg_classes.tsv
• ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/genomes-pipeline/ncrna/
• ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/genomes-pipeline/continent_countries.csv
• https://data.gtdb.ecogenomic.org/releases/release207/207.0/auxillary_files/gtdbtk_r207_v2_data.tar.gz

Containers

This pipeline requires singularity or docker as the container engine to run pipeline.

The containers are hosted in biocontainers and quay.io/microbiome-informatics repository.

It's possible to build the containers from scratch using the following script:

cd containers && bash build.sh

Running the pipeline

Data preparation

1. You need to pre-download your data to directories and make sure that genomes are uncompressed. Scripts to fetch genomes from ENA (fetch_ena.py) and NCBI (fetch_ncbi.py) are provided and need to be executed separately from the pipeline. If you have downloaded genomes from both ENA and NCBI, put them into separate folders.

2. When genomes are fetched from ENA using the fetch_ena.py script, a CSV file with contamination and completeness statistics is also created in the same directory where genomes are saved to. If you are downloading genomes using a different approach, a CSV file needs to be created manually (each line should be genome accession, % completeness, % contamination). The ENA fetching script also pre-filters genomes to satisfy the QS50 cut-off (QS = % completeness - 5 * % contamination).

3. You will need the following information to run the pipeline:

• catalogue name (for example, zebrafish-faecal)
• catalogue version (for example, 1.0)
• catalogue biome (for example, root:Host-associated:Human:Digestive system:Large intestine:Fecal)
• min and max accession number to be assigned to the genomes (only MGnify specific). Max - Min = #total number of genomes (NCBI+ENA)

Execution

The pipeline is built in Nextflow, and utilized containers to run the software (we don't support conda ATM). In order to run the pipeline it's required that the user creates a profile that suits their needs, there is an ebi profile in nexflow.config that can be used as template.

After downloading the databases and adjusting the config file:

nextflow run EBI-Metagenomics/genomes-pipeline -c  -profile  \
--genome-prefix=MGYG \
--biome="root:Host-associated:Fish:Digestive system" \
--ena_genomes= \
--ena_genomes_checkm= \
--mgyg_start=0 \
--mgyg_end=10 \
--catalogue_name=zebrafish-faecal \
--catalogue_version="1.0" \
--ftp_name="zebrafish-faecal" \
--ftp_version="v1.0" \
--outdir=""

Development

Install development tools (including pre-commit hooks to run Black code formatting).

pip install -r requirements-dev.txt
pre-commit install

Code style

Use Black, this tool is configured if you install the pre-commit tools as above.

To manually run them: black .

Testing

This repo has 2 set of tests, python unit tests for some of the most critical python scripts and nf-test scripts for the nextflow code.

To run the python tests

pip install -r requirements-test.txt
pytest

To run the nextflow ones the databases have to downloaded manually, we are working to improve this.

nf-test test tests/*