Comparative genomics automation and standardization software
Project description
PURPOSE
Bring broadscale comparative genomics to the masses. Operational with prokaryote and fungal genome data - generalized taxonomy-agnostic integration on the way.
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
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