mycotools 0.31.36

Comparative genomics automation and standardization software

NOTE

This software is a beta release - kindly raise an issue for errors.

PURPOSE

Bring broadscale comparative genomics to the masses.

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

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

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INSTALL

Please review the wiki for installation and usage information!