A compilation of bioinformatic and computation biology inspired python tools
Project description
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 konkelzach@protonmail.com
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 fasta
s 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.
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