Skip to content
Fowler Lab
Fowler Lab

Predicting antibiotic resistance de novo

  • News
  • Research
    • Overview
    • Manifesto
    • Software
    • Reproducibility
    • Publications
  • Members
  • Teaching
  • Contact
    • PhDs
  • Wiki
Fowler Lab
Fowler Lab

Predicting antibiotic resistance de novo

SARS-CoV-2 pipeline live on EIT Pathogena

Philip Fowler, 28th January 202528th January 2025

Back in the SARS-CoV-2 pandemic we worked closely with ORACLE Corp to build and deploy a bioinformatics pipeline in ORACLE Cloud that processes raw genetic files and infers what the consensus genome is and hence what lineage (e.g. BA.2) it belongs to. The heart of the pipeline is an amplicon-aware variant caller, viridian, that was written by Zamin Iqbal’s group and there is a nice preprint out showing how it avoids various calling artefacts that can complicate phylogenetic tree construction.

An improved version of the pipeline has now been deployed, tested and launched on EIT Pathogena, a cloud-based genetics platform. Anyone can sign up and process at least 1,000 samples for free.

Share this:

  • Click to share on X (Opens in new window) X
  • Click to share on Bluesky (Opens in new window) Bluesky
  • Click to email a link to a friend (Opens in new window) Email
  • Click to share on LinkedIn (Opens in new window) LinkedIn
  • Click to share on Mastodon (Opens in new window) Mastodon

Related

clinical microbiology

Post navigation

Previous post
Next post

Related Posts

clinical microbiology

Our World in Data

10th January 202410th January 2024

I didn’t know that Our World in Data was also based at the University of…

Share this:

  • Click to share on X (Opens in new window) X
  • Click to share on Bluesky (Opens in new window) Bluesky
  • Click to email a link to a friend (Opens in new window) Email
  • Click to share on LinkedIn (Opens in new window) LinkedIn
  • Click to share on Mastodon (Opens in new window) Mastodon
Read More

New preprint: a deep learning model that can read 96-well broth micro dilution plates

23rd February 202523rd February 2025

The CRyPTIC project used bespoke 96-well broth microdilution plates to measure the minimum inhibitory concentrations…

Share this:

  • Click to share on X (Opens in new window) X
  • Click to share on Bluesky (Opens in new window) Bluesky
  • Click to email a link to a friend (Opens in new window) Email
  • Click to share on LinkedIn (Opens in new window) LinkedIn
  • Click to share on Mastodon (Opens in new window) Mastodon
Read More
antimicrobial resistance

AMyGDA now available from GitHub

27th January 202027th January 2020

AMyGDA is a python module that analyses photographs of 96-well plates and, by examining each…

Share this:

  • Click to share on X (Opens in new window) X
  • Click to share on Bluesky (Opens in new window) Bluesky
  • Click to email a link to a friend (Opens in new window) Email
  • Click to share on LinkedIn (Opens in new window) LinkedIn
  • Click to share on Mastodon (Opens in new window) Mastodon
Read More

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Privacy & Cookies: This site uses cookies. By continuing to use this website, you agree to their use.

To find out more, including how to control cookies, see here: Cookie Policy
    ©2025 Fowler Lab | WordPress Theme by SuperbThemes