aggreen-MTB-CNN

The model was taken from Green & Yoon et al., Nat Comms (2022).

The start and end coordinates of the 13 target loci can be found in data_files/target_loci.csv or queried from the container by passing the --get-target-loci argument (see below). Consensus sequences from raw reads can be created with this Docker container

Example usage

Get coordinates of target loci

docker run -v $PWD:/data \
    julibeg/tb-ml-aggreen-mtb-cnn:v0.1.0 \
    --get-target-loci \
    -o nn_target_loci.csv

Predict resistance against 13 drugs from target consensus sequences (passed as FASTA file)

docker run -v $PWD:/data \
    julibeg/tb-ml-aggreen-mtb-cnn:v0.1.0 \
    input_seqs.fa