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
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.
mtdb u --init <DIR>mtdb u --updategffformats into a consistent standard.mtdbdatabase format is a uniform input for analyses with 100,000s to as few as a single genomeINSTALL
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