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.