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nomadic

Overview

Nomadic is a real-time bioinformatics pipeline and dashboard for nanopore sequencing data. While sequencing is still ongoing, it performs read mapping and sample quality control, as well as variant calling and annotation. This information is displayed in real-time to a graphical dashboard that has interactive features.

dashboard

It was designed to work with amplicon sequencing data from the NOMADS-MVP protocol, which targets a panel of genes important for the control of Plasmodium falciparum malaria (see Basic Usage). However, it was coded flexibly and works with other organisms or amplicon panels (see Advanced Usage).


example


Features

  • Real-time read mapping with Minimap2.
  • Real-time sample quality control and amplicon coverage evaluation.
  • Real-time variant calling with bcftools. These calls are preleiminary; treat with caution.
  • Support for different reference genomes or amplicons panels.

Resources

  • The NOMADS-MVP protocol is available in English and French.
  • Read our preprint here.

Acknowledgements

This work was funded by the Bill and Melinda Gates Foundation (INV-003660, INV-048316).