This is a tb-profiler plugin that will enable the use of clair3 as a variant caller in tb-profiler (and more broadly, any tool using (pathogen-profiler)[https://github.com/jodyphelan/pathogen-profiler]).

Run the following code from within the conda environment where you have already installed tb-profiler.

mamba install bioconda::clair3
pip install git+https://github.com/jodyphelan/tb-profiler-clair3.git

You will now have access to tb-profiler-clair3 which is a tool you can use to view and download available models to use during variant calling.

To view the list run:

tb-profiler-clair3 list 

To download a model run:

tb-profiler-clair3 download --model r1041_e82_400bps_sup_v500

Or if you prefer you can download all models with:

tb-profiler-clair3 download --all

Now you should be ready to use clair3 in tb-profiler. Youll need to specify --caller clair3 and the appropriate model, e.g. --clair3_model r1041_e82_400bps_sup_v500. Here is an example:

tb-profiler profile --platform nanopore --caller clair3 -1 reads.fastq.gz --clair3_model r1041_e82_400bps_sup_v500 -t 8 --prefix my_sample