Learning path topics
-
Module: AMR gene detection
AMR gene content can be assessed from the contigs to detect known resistance mechanisms and potentially identify novel mechanisms.
Time estimation: 2 hours
Learning objectives:
- Run a series of tool to assess the presence of antimicrobial resistance genes (ARG)
- Get information about...
-
Module: Assembly
Assembly is a major step in the process of detecting AMR genes as it combines sequenced reads into contigs, longer sequences where it will be easier to identify genes and in particular AMR genes
Time estimation: 4 hours
Learning objectives:
- Run tools to evaluate sequencing data on...
-
Module: Genome annotation
The generated contigs can be annotated to detect genes, potential plasmids, etc. This will help the AMR gene detection process, especially the verification and visualization
Time estimation: 3 hours
Learning objectives:
- Run a series of tool to annotate a draft bacterial genome for...
-
Module: Species and contamination checking
Quality control and taxonomic assignation is useful in AMR detection to verify the quality of the data but also to check contamination and confirm species
Time estimation: 2 hours
Learning objectives:
- Run tools to evaluate sequencing data on quality and quantity
- Evaluate the output...
-
Recommended follow-up tutorials
Time estimation: 4 hours
Learning objectives:
- Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore data
- Preprocess the sequencing data to remove adapters, poor quality base content and host/contaminating reads
- Perform taxonomy profiling indicating and...