Bring broadscale comparative genomics to the masses. Taxonomy-agnostic, with automated data acquisition operational with prokaryote, animal, plant, and fungal genome data.
Mycotools is a compilation of computational biology tools and database (MycotoolsDB/MTDB) software that facilitate large-scale comparative genomics. MycotoolsDB dereplicates and locally assimilates NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles.
- Database initialization:
mtdb u --init <DIR> - Database updating:
mtdb u --update - The MycotoolsDB (MTDB) uniformly curates GenBank/MycoCosm and local
gffformats into a consistent standard - The
.mtdbdatabase format is a uniform input for analyses with 100,000s to as few as a single genome - Mycotools software suite includes modules to automate routine-complex comparative genomics, such as phylogenetic analysis
Please review the wiki for installation and usage information!
If Mycotools contribute to your analysis, please cite the preprint and mention the version in-line.
Konkel, Z., Slot, J. C. Mycotools: An Automated and Scalable Platform for Comparative Genomics. bioRxiv 2023.09.08.556886; doi: https://doi.org/10.1101/2023.09.08.556886