AMR prediction in Mycobacterium tuberculosis using whole genome sequences
install the code using git
git clone https://github.com/Ankitapal1995/TB-AMRpred.git
requirement
cd TB-AMRpred
conda env create -f environment_amr.yml
or
manually create environment
miniconda3=24.1.2
python=3.12.0
snippy=4.6.0
numpy==1.26.4
pandas==2.2.1
matplotlib==3.8.3
scikit-learn==1.4.2
xgboost==2.0.3
pip=24.0
activate conda environment
conda activate amr
add path after installation
open TB-AMRpred file and add your path
path='your path to the TB-AMRpred'/scripts
go to scripts folder
cd scripts
open paths_variable.py and add your path
path='your path to the TB-AMRpred'
script run using whole genome fasta sequence
sh TB-AMRpred input.fasta
or
sh TB-AMRpred input.fna
script run using whole genome fastq sequence
sh TB-AMRpred input_1.fastq.gz input_2.fastq.gz