https://github.com/mbhall88/head_to_head_pipeline

Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.
https://github.com/mbhall88/head_to_head_pipeline

bioinformatics clustering diagnostics drug-resistance illumina nanopore pipeline snakemake transmission tuberculosis

Last synced: 28 days ago
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Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.

• Host: GitHub
• URL: https://github.com/mbhall88/head_to_head_pipeline
• Owner: mbhall88
• License: gpl-3.0
• Created: 2019-02-07T16:54:54.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2023-01-05T21:39:14.000Z (almost 2 years ago)
• Last Synced: 2024-10-14T13:14:18.807Z (2 months ago)
• Topics: bioinformatics, clustering, diagnostics, drug-resistance, illumina, nanopore, pipeline, snakemake, transmission, tuberculosis
• Language: Jupyter Notebook
• Homepage:
• Size: 501 MB
• Stars: 5
• Watchers: 4
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
### 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][doi].

[doi]: https://doi.org/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](https://snakemake.github.io/)

- [Conda](https://docs.conda.io/en/latest/) (and

  [Mamba](https://github.com/mamba-org/mamba))

- [Singularity](https://sylabs.io/docs)

- The Python library [`pandas`](https://pandas.pydata.org/)

See subdirectories for more specific information about different pipelines. They are

nested according to their dependence on the outputs of each pipeline.

- [Quality Control](data/QC)

  - [Assembly](analysis/assembly)

  - [Baseline variant analysis](analysis/baseline_variants)

    - [Transmission clustering](analysis/transmission_clustering)

  - [Drug Resistance Prediction](analysis/resistance_prediction)

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

- [H37Rv PRG construction](data/H37Rv_PRG)

- [Pandora variant analysis](analysis/pandora_variants)

# 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 .

The raw Nanopore data is available to download from: . See the sample metadata file for mappings between samples and the relevant Nanopore runs and barcode numbers.