Quickstart
Installation
Install using pip:
pip install git+https://github.com/bloodhound-devs/bloodhound.git
Usage
See the options for making inferences with the command:
bloodhound --help
Model
wget https://figshare.com/ndownloader/files/54720671?private_link=5f43c8fc6f157f3111e3 -O bloodhound.zip
unzip bloodhound.zip
Run
bloodhound --checkpoint bloodhound.r226.ckpt --hmm-models-dir markers --output-csv GCA_000006945.csv --input GCA_000006945.2.fna
Training
You can train the model on releases from GTDB or your own custom dataset. See the instructions in the documentation for preprocessing and training.