Interesting choice of short read assembly, SKESA, which was built to enable fast and accurate assemblies for MLST typing, but has inherent problems with plasmids where we find most AMR genes.

[http://www.dtu.dk/-/media/DTU_Generelt/Andet/mail-signature-logo.png] Philip Thomas Lanken Conradsen Clausen Postdoc National Food Institute plan@food.dtu.dkmailto:plan@food.dtu.dk Kemitorvet Building 204 2800 Kgs. Lyngby www.food.dtu.dkhttp://www.food.dtu.dk/ ________________________________ Fra: Marco van Zwetselaar via Bioinfo List bioinfo-list@seqshare.org Sendt: 30. juli 2024 10:26 Til: bioinfo-list@seqshare.org bioinfo-list@seqshare.org Emne: [Bioinfo-list] Yet another AMR pipeline: AMRomics

AMRomics: a scalable workflow to analyze large microbial genome collections https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10620-8

Two interesting features (vis a vis other pipelines): support for Nanopore reads, and construction of phylogenetic trees from core-genomes of the data.

Cheers, Marco

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