A compilation of bioinformatic and computation biology inspired python tools
Project description
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
fasta
s 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.
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