mycotools 1.0.0

Comparative genomics automation and standardization software

PURPOSE

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 gff formats into a consistent standard
• The .mtdb database 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

INSTALL

Please review the wiki for installation and usage information!

CITING

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

---