Analysis pipeline for Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination and Drug Susceptibility Prediction (DOI to come).
The decontaminated fastq files for each isolate have been deposited in the European Nucleotide Archive (ENA) under the Project accession PRJEB56100. A data sheet mapping accessions to study information can additionally be found at https://doi.org/10.6084/m9.figshare.21193588.
To run the pipeline you will need snakemake, conda/mamba, and singularity.