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.
Philip Thomas Lanken Conradsen Clausen
Postdoc
National Food Institute
Kemitorvet
Building 204
2800 Kgs. Lyngby
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


_______________________________________________
Bioinfo List mailing list -- bioinfo-list@seqshare.org
To unsubscribe send an email to bioinfo-list-leave@seqshare.org