This is the collection of scripts used for the "CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut" by Avershina et al, 2026 preprint
This repository contains code and data processing workflows used for the extended microbiome repository generation and bacteria-MGE interaction analysis using CRISPR-Cas.
cctyper_snakemake_wf/ : Snakemake workflow for CRISPR-Cas data generation using CRISPRCasTyper
scapp_snakemake_wf/ : Snakemake workflow for plasmid data generation using SCAPP
data_analysis/ : Scripts used for processing of generated data
- Raw sequencing data are available from The Federated European Genome-phenome Archive (FEGA): accession EGAS50000000170
- Prokaryotic metagenome-assembled genomes were described in Birkeland et al, 2025 and generated using ATLAS
- Viral data were described in Istvan et al, 2026 and generated using VirMake
- Processed fastafiles and metadata are deposited in Figshare
- Python ≥ 3.9
- pandas
- numpy
- scikit-learn
- biopython
- stats
- matplotlib
- seaborn
- cctyper
- scapp
Ekaterina Avershina
University of Oslo
Email: ekateria@uio.no
Trine B Rounge
University of Oslo
Email: t.b.rounge@uio.no