mycotools 0.9b2

A compilation of bioinformatic and computation biology inspired python tools

PURPOSE

Mycotools is a compilation of computational biology tools and database (MycotoolsDB) software designed to increase throughput analyzing fungal genomic data (JGI & NCBI). MycotoolsDB is a database schema with uniform file curation, scalability, and automation as guiding principles. Installation as simple as updateDB.py --init <DIR>. Updates by assimilating the most recent JGI & NCBI data to manipulate locally via updateDB.py -u. Scalability enables analyses with datasets of 1000s of fungi to as few as 1 or 2 simply by inputting a full database .db file or an extracted .db portion. MycotoolsDB is not available outside of the Ohio Supercomputer Center until we publish the tools. Please email [e-mail] if you are interested.

By integrating with the curated MycotoolsDB, Mycotools cuts time on routine tasks like retrieving gff or fasta accessions, running and compiling fastas of MycotoolsDB BLAST/hmmsearches, automated phylogenetic pipelines, and database manipulation tools. 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.