Vaginal Microbial Genome Collection (VMGC) MIDAS-compatible pangenome database

This is a MIDAS-compatible pangenome database constructed from the Vaginal Microbial Genome Collection (VMGC). Installation 1. Download the database wget https://zenodo.org/records/18355814/files/VMGC_MIDAS_db.tar.gz 2. Uncompress the database Note: Uncompressed size = 59GB tar -zxf VMGC_MIDAS_db.tar.gz 3. Specify the database path in MIDAS commands midas [command_name] [other arguments] --midasdb_dir /path/to/db/location/VMGC_MIDAS_db --midasdb_name localdb Citation Please cite our paper if you use this database: Dubin CA, Zhao C, Pollard KS, Oskotsky T, Golob JL, Sirota M. Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia. bioRxiv. Preprint posted online September 11, 2025:2025.09.11.675634. doi:10.1101/2025.09.11.675634 Additional Resources MIDAS: https://github.com/pollardlab/MIDAS VMGC: https://www.nature.com/articles/s41564-024-01751-5 Pipline for constructing a custom database: https://github.com/clairedubin/MIDASv3_nextflow