Introduction

MTBseq-nf: Enabling Scalable Tuberculosis Genomics “Big Data” Analysis Through a User-Friendly Nextflow Wrapper for MTBseq Pipeline

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

nextflow run mycobactopia-org/MTBseq-nf \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

mycobactopia-org/MTBseq-nf was originally written by Abhinav Sharma (@abhi18av) and Davi Marcon (@mxrcon).

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Documentation

For detailed instructions on installation, usage, and output interpretation, please refer to the documentation.

Citations

If you use mycobactopia-org/MTBseq-nf for your analysis, please cite it using the following publication:

Sharma, A.; Marcon, D.J.; Loubser, J.; Lima, K.V.B.; van der Spuy, G.; Conceição, E.C. MTBseq-nf: Enabling Scalable Tuberculosis Genomics "Big Data" Analysis Through a User-Friendly Nextflow Wrapper for MTBseq Pipeline. Microorganisms 2025, 13, 2685. https://doi.org/10.3390/microorganisms13122685

BibTeX entry:

@article{Sharma2025,
   author = {Sharma, Abhinav and Marcon, Davi Josué and Loubser, Johannes and Lima, Karla Valéria Batista and van der Spuy, Gian and Conceição, Emilyn Costa},
   title = {MTBseq-nf: Enabling Scalable Tuberculosis Genomics "Big Data" Analysis Through a User-Friendly Nextflow Wrapper for MTBseq Pipeline},
   journal = {Microorganisms},
   volume = {13},
   number = {12},
   ISSN = {2076-2607},
   DOI = {10.3390/microorganisms13122685},
   year = {2025},
   type = {Journal Article}
}

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.