mycotools 0.5.6

A compilation of bioinformatic and computation biology inspired python tools

NOTE

This software is a beta release (prokaryote is alpha state) - errors are expected. Kindly report them. If you can find the bug, even better! The goal is to reach a longterm stable release, though maintaining the software for my use is currently the priority.

PURPOSE

Bring broadscale comparative genomics to the masses.

Mycotools is a compilation of computational biology tools and database MycotoolsDB software that facilitate large-scale fungal comparative genomics. MycotoolsDB locally assimilates all NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles.

• Database initialization is as simple as mtdb u --init <DIR>
• mtdb u --update brings the database to the current date
• The MycotoolsDB (MTDB) uniformly curates the numerous iterations of the gff, allowing for reliable analyses and format expectations from multiple eras
• The .mtdb database format enables swift transitions from analyses with datasets of 100,000s genomes to as few as a lineage of interest
• The MycotoolsDB can be adminstered by one administrator and accessed by multiple users that integrate via mtdb -i <DB_DIR>

Mycotools facilitates routine-complex tasks like retrieving locus, gff, or fasta accessions; running and compiling fastas of MycotoolsDB BLAST/hmmsearches; 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. Please see the USAGE guide for more information.

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.