Version

Pipeline Version

1.5.0

Software Dependencies

The pipeline integrates several bioinformatics tools. Specific versions used in your run are automatically captured in the software_versions.yml.

Reference Data

TB Reference Genome

  • Strain: Mycobacterium tuberculosis H37Rv

  • Accession: NC_000962.3

  • Description: The standard reference genome used for coordinate mapping and variant calling.

Mutation Catalogue

Lineage Barcodes

  • Source: TBProfiler SNP Panel

  • Repository: jodyphelan/TBProfiler

  • Description: A curated set of SNPs used for phylogenetic lineage and sub-lineage classification.

Changelog

1.5.0

  • Upload to FHIR server using Auth2, including helper script: get_access_token.py

  • expanded metadata CSV to fill the FHIR resources.

1.4.0

The Deeplex workflow has been deprecated.

References

  1. World Health Organization. (2023). Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance, 2nd ed. WHO Publication

  2. Phelan, J. E., et al. (2019). Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Medicine.

  3. Napier, G., et al. (2020). Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies. Genome Medicine.

  4. Di Tommaso, P., et al. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology.

  5. Li, H., et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics

  6. Genomics Reporting Implementation Guide v3.0.0. Variant Reporting.