This is the repository of the analysis scripts and methods that were used in the paper Multicenter analysis of sputum microbiota in tuberculosis patients published in PlosONE.
The repository is organised by cohort. While we tried to provide as much details as possible, the repository is not entirely self-contained, i.e. most steps describled here start from processed reads. Raw reads are available at Sequence Read Archive under accession number PRJNA611472.