diff --git a/learning-pathways/amr-gene-detection.md b/learning-pathways/amr-gene-detection.md index 2a4b808b038130..ace9b81efda96b 100644 --- a/learning-pathways/amr-gene-detection.md +++ b/learning-pathways/amr-gene-detection.md @@ -2,7 +2,7 @@ layout: learning-pathway title: Detection of AMR genes in bacterial genomes description: | - Learn how to identify AMR genes in bacterial genomes + This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy. type: use tags: [amr, bacteria, microgalaxy, one-health] @@ -11,7 +11,6 @@ editorial_board: funding: - abromics - pathway: # - section: "Module 1: Introduction" # description: | @@ -20,33 +19,38 @@ pathway: # # - name: introduction # # topic: genome-annotation - - section: "Module: AMR gene detection in bacterial isolates (short reads)" +# - section: "Module: Taxonomy assignation" +# description: | +# Taxonomic assignation is useful in AMR detection to check contamination and confirm species +# tutorials: +# - name: taxonomy +# topic: ecology + + - section: "Module: Assembly" description: | - + Assembly is a major step in the process to detect AMR genes as it combines sequenced reads into contigs, longer sequences where it will be easier to identify genes and in particular AMR genes tutorials: - name: mrsa-illumina topic: assembly - - name: amr-gene-detection - topic: genome-annotation - -# - section: "Module 3: AMR gene detection in bacterial isolates (long reads)" -# description: | -# -# tutorials: # - name: mrsa-nanopore # topic: assembly -# - name: amr-gene-detection -# topic: genome-annotation -# -# - section: "Module 4: AMR gene detection in bacterial isolates (long and short reads)" +# - name: hybrid-assembly +# topic: assembly + +# - section: "Module: Genome annotation" # description: | -# +# The generated contigs can be then annotated to detect genes, potential plasmid, etc. This will help the AMR gene detection process, specially the verification and the visualization # tutorials: -# #- name: hybrid-assembly -# # topic: assembly -# - name: amr-gene-detection +# - name: bacterial-genome-annotation # topic: genome-annotation + - section: "Module: AMR gene detection" + description: | + + tutorials: + - name: amr-gene-detection + topic: genome-annotation + - section: "Recommended follow-up tutorials" tutorials: - name: pathogen-detection-from-nanopore-foodborne-data