mycotools 0.5.1

A compilation of bioinformatic and computation biology inspired python tools

Now alpha support for prokaryotes too!

NOTE

While extensive alpha testing has been conducted, this software is in a beta state, and errors are expected. Kindly report these issues and remain patient for fixes - if you can find the bug, even better! This software will have longterm maintenance, although my focus is on my own research.

Cheers, Zachary Konkel

PURPOSE

Bring broadscale comparative genomics to the masses.

Mycotools is a compilation of computational biology tools and database MycotoolsDB software that facilitate large-scale prokaryote and 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.

• Installation is as simple as updateDB.py --init <DIR>. No more limited and incomplete databases.
• updateDB.py --update brings the database to the current date. No more database obsolecence in the wake of accelerating genome availability.
• The MycotoolsDB (MTDB) uniformly curates the numerous notorious 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. No more scrambling to acquire files for an analysis.

Mycotools is currently available as a beta subset of the full suite, excluding the database assimilation tools. MycotoolsDB is currently restricted to Ohio Supercomputer Center - 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.