normalize and verify genomic data
Project description
creating, searching, and analyzing phylogenetic signatures from genomes or reads of DNA.
Prerequisites
Python 3.6 or greater is required.
Run-time dependencies of bionorm are :
biopython, click, ruamel.yaml, and sequencetools.
bionorm uses the poetry dependency manager
Installation
This package is tested under Linux and MacOS using Python 3.7. install via pip (or pip3 under some distributions) :
pip install bionorm
If you wish to develop bionorm, download a release and in the top-level directory:
pip install --editable .
If you wish to have pip install directly from git, use this command:
pip install git+https://github.com/ncgr/bionorm.git
Usage
Installation puts a single script called bionorm in your path. The usage format is:
bionorm [GLOBALOPTIONS] COMMAND [COMMANDOPTIONS] [ARGS]
A listing of commands is available via bionorm --help. Current available commands are:
busco |
Perform BUSCO checks. |
detector |
Detect/correct incongruencies among files. |
fasta |
Check for GFF/FASTA consistency. |
generate_readme |
Generates a README file with details of genome. |
index |
Indexes FASTA file. |
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