Protocols – EMBARK

As the project proceeds, we will add our proposed protocols and any additional data to this page.

EMBARKFollow

A @JPIAMR funded program to improve monitoring of antimicrobial resistance in the environment

This is a lecture that I gave @CCDD_HSPH a few months ago that gives a good overview of recent work that we have done on evolutionary drivers of AMR in real world pathogen populations - mainly unpublished
https://www.youtube.com/watch?v=-lQt_9awbmg

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Luis Pedro Coelho🌻@luispedrocoelho·

24 Jun

Very few tools/projects seem to be running rgi in the more conservative mode

(even if they think they are—I know I personally was not aware of this nuance until @svetlana_up started digging into it and showed me)

https://github.com/search?q=rgi+main&type=code https://twitter.com/svetlana_up/status/1539997813987221509

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Johan BengtssonPalme @bengtssonpalme·

23 Jun

Many years ago, I learnt about this thing called Future Research Leaders - a type of grant you’d only get if you were a particularly promising young researcher. It’s a strange (but good) feeling to now be named one of them this year. https://twitter.com/strategiskaSSF/status/1539176118929997825

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EMBARK @EMBARK_JPIAMR·

24 Jun

.@svetlana_up @luispedrocoelho
(@BigDataBiology) wrote an important blogpost from their experience on metagenomic annotation of antibiotic resistome:

If you are using RGI for your resistome study, you probably want --exclude_nudge

Svetlana U. Perović@svetlana_up

I love to use RGI @arpcard (&other tools!) for metagenomic annotation but you should be careful w/DEFAULT run

BLASTP is much more sensitive vs DIAMOND & finds these hits that should've never been reported (e-value>1) & RGIdefault promotes them to Strict
👉https://www.big-data-biology.org/blog/2022/06/23/exclude_nudge/

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