Awesome

Paper

Hall, M. B. et al. Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis. The Lancet Microbe 0, (2022) doi: 10.1016/S2666-5247(22)00301-9.

This repository holds the pipelines/scripts used for our paper analysing Illumina and Nanopore for M.tuberculosis drug resistance calling and transmission clustering.

For people wanting to analyse their Nanopore data in the same manner as we did in this paper, we would suggest using https://github.com/mbhall88/tbpore, which is a python program that runs the drug resistance prediction and clustering (with a smaller decontamination database) components of this pipeline. It is actively maintained and much easier to use.

All pipelines require the following dependencies to be installed:

• Snakemake
• Conda (and Mamba)
• Singularity
• The Python library pandas

See subdirectories for more specific information about different pipelines. They are nested according to their dependence on the outputs of each pipeline.

• Quality Control
  • Assembly
  • Baseline variant analysis
    • Transmission clustering
  • Drug Resistance Prediction

The following pipelines are not relevant to the work in the final paper.

• H37Rv PRG construction
• Pandora variant analysis

Data availability

All data is submitted under the Project accession PRJEB49093.

The accessions and all relevant sample metadata for this study can be found at https://doi.org/10.6084/m9.figshare.19304648.

The raw Nanopore data is available to download from: https://ftp.ebi.ac.uk/pub/databases/ont_tb_eval2022/. See the sample metadata file for mappings between samples and the relevant Nanopore runs and barcode numbers.