SIB resource candidate: Nextstrain


Richard Neher
Biozentrum & SIB, University of Basel


slides at neherlab.org/202104_SIB_resource.html

Origins of Nextstrain

  • Started as an influenza specific project in 2015
  • Meant to accompany attempts to predict future influenza population with "always up-to-date" trees and predictions
  • Initially a project of Trevor Bedford and myself
  • Expansion beyond influenza (Ebola, Mers, Zika)

Nextstrain is both a tool chain and a web-app

Core tools by nextstrain

  • Augur -- extensible phylodynamics pipeline
    • composible, modular, and extensible
    • wrappers for alignment, tree building, etc
    • phylodynamic and phylogeographic modules
    • custom modules for frequency and fitness estimation
  • Auspice -- interactive visualization
    • Tree viewer, map module, flexible frequencies, charts, filters...
    • Customizable and available for white labeling
    • powers nextstrain.org
  • of course completely open
  • workflows and data (to the extend that we are allowed) open
  • extensive documentation
    •

Analyses maintained by the Nextstrain

Nextstrain-hosted community resources

Community builds via github

SARS-CoV-2 analyses by the community

Nextstrain in the pandemic

  • ever increasing data volumes
  • massive public interest and media coverage
  • rapidly shifting requirements

Usage in Public Health and Academia

In-house use by public health stake holders

  • US CDC
  • Robert-Koch-Institut
  • RIVM -- Dutch public health institute
  • ECDC
  • GISAID
  • Seq-COVID Spain
  • Broad Institute
  • Chan Zuckerberg Institute
  • and many more...

Enabling other tools

  • CoVariants.org by Emma Hodcroft
  • SPSP by SIB

New developments

Plans and outlook

Basel focussed efforts

  • Nextclade
    • Effortless first analysis of new data
    • Client based and 100% privacy preserving
    • Speed-up via RUST and WASM
    • Extend to other viruses
  • TreeTime refactor
    • workhorse of much of augur
    • computational bottleneck
    • huge scope for algorithmic and implementation improvements
  • Reassortment, recombination, and other non-tree-like evolution

Joint or Seattle focussed efforts

  • Cloud computing
    • Allow users to run their analysis via a web interface
    • Host user spaces
    • Integrated with Pathogen Genomics initiative of the Gates Foundation
  • auspice and nextstrain.org
    • More visualization components
    • Data set discovery options
  • Documentation
  • Pathogen specific dashboards
    • Integration with serological and high throughput data
    •

Basel

  • Ivan Aksamentov (Software Engineer)
    • Nextclade
    • Nextclade
    • CoVariants
    • Covid19-Scenarios
  • Bioinformatician (N.N.)
  • Emma Hodcroft (former post-doc, now Bern)
  • Moira Zuber (Student assistent, running analyses)
  • Benjamin Otter (Student assistent, augur dev)
  • Research led by myself involving 2FTEs

Seattle/NZ

  • Trevor Bedford (PI)
  • Tom Sibley (Software engineer)
  • John Huddleston (former PhD Student/research scientist)
  • James Hadfield (Software/frontend)
  • Jover Lee (bioinformatics)
  • Eliah Harkins (frontend/builds)

Basel

  • Uni Basel/Biozentrum core funding
  • Open Science Prize 2017
  • Special SARS-CoV-2 call from the SNF (joint grant with Bern)
  • Future: funding from BAG through WGS Surveillance initiative

Seattle/NZ

  • Open Science Prize 2017
  • Research grants
  • Philantropy