mycotools 0.13

A compilation of bioinformatic and computation biology inspired python tools

PURPOSE

Bring the power of broadscale genomic analyses to the masses. Mycotools is a compilation of computational biology tools and database (MycotoolsDB) software designed to increase throughput analyzing fungal genomic data (JGI, NCBI, and user-inputted). MycotoolsDB is a database schema with uniform file curation, scalability, and automation as guiding principles. Installation is as simple as updateDB.py --init <DIR>. Updates assimilate the most recent JGI & NCBI locally via updateDB.py -u. Scalability enables swift transitions from analyses with datasets of 1000s of fungi to as few as 1 or 2 simply by inputting a full database .mtdb file or an extracted .mtdb obtained via extractDB.py.

Mycotools is currently available as a subset of the full suite, excluding the database assimilation tools. MycotoolsDB is not available outside of the Ohio Supercomputer Center until we publish a manuscript using the tools (expected summer 2022). If you are interested in early access, please email [e-mail].

By integrating with the curated MycotoolsDB, Mycotools aids routine-complex tasks like retrieving gff or fasta accessions; running and compiling fastas of MycotoolsDB BLAST/hmmsearches; biology-based database manipulation tools; automated phylogenetic analysis pipelines from blast to Pfam extraction to tree prediction, etc etc. Mycotools includes sets of utilities that also enable easy acquisition of batches of sequence data using ncbiDwnld.py and jgiDwnld.py.

USAGE

Check out README.md for install and the USAGE.md for a guide.

CITING

If Mycotools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the Mycotools version in line.