Next is Maido Remm presenting how DNA sequencing can be used for typing and diagnostics: StrainSeeker works similarly as Kraken. I wonder if it has the same issues as Kraken does? It’s cool to hear something new even after 4 days spent on this topic at IMMEM XIV.
#EYSF2025

Even though Cas9 technology is promising in many fields, including gene therapy, it still has many limitations to overcome before its’ full potential can be used. For example, different Cas nucleases require different PAM sequences for cleavage to happen which Šikšnys lab is now working on solving.

The last presentation is by Val Fernandez Lanza about BacTaxID - genome-based, scalable, hierarchical, heuristic bacterial typing method. Similar to LIN and EC codes. The shark is very excited for the upcoming poster session.

Next, Verónica Mixão is presenting ReporTree for linking pathogen genetic clusters with epidemiological dat and how it can implement wgMLST data for extra resolution.

It’s incredible how much a great team of scientists can do in just a fee days!

It covered QC guidelines, assembly graph interpretation, metagenomics, microbial typing specifications, AllTheBacteria workflow implementation on nextflow and interactive and easy-to-use AMR exploration of AllTheBacteria, and plasmid outbreak reporting.

So it’s even higher than I thought! Achromobacter is a mess and >10% have wrong species metadata but I hoped that it’s a more isolated problem.

Also, I am attending the conference with the little shark given by my son so I wouldn’t be bored. Today we managed to get to the ocean before the start of the day and enjoy the beauty of Porto.

GTDB sometimes assigns suffixes for non monophyletic taxa where historically the classification is misleading or ambiguous. And we should all do better when submitting our genomes to public databases and naming species.