Bacterial genomics and AMR detection

This track explains the basic steps to (1) process, assemble, annotate a bacterial genome and (2) detect Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.

Organisers(s) orcid logoBérénice Batut avatar Bérénice Batutorcid logoClea Siguret avatar Clea Siguret
Instructor(s) orcid logoBérénice Batut avatar Bérénice Batutorcid logoClea Siguret avatar Clea Siguretorcid logoSaim Momin avatar Saim Mominorcid logoEngy Nasr avatar Engy NasrMeltem Kutnu avatar Meltem Kutnuorcid logoPaul Zierep avatar Paul Zierep

Bacterial genomics

Preparation, assembly and annotation of a bacterial genome. If you encounter any issue please ask us in this Slack channel.

Lesson Slides Hands-on Recordings
Quality and contamination control in bacterial isolate using Illumina MiSeq Data
illumina bacteria microgalaxy
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
illumina assembly microgalaxy
Bacterial Genome Annotation
gmod illumina bacteria microgalaxy jbrowse1

AMR detection

Detect Antimicrobial resistance (AMR) genes in an assembled bacterial genome. If you encounter any issue please ask us in this Slack channel.

Lesson Slides Hands-on Recordings
Identification of AMR genes in an assembled bacterial genome
gmod illumina amr one-health jbrowse1 microgalaxy

Pathogen detection

Pathogen detection. If you encounter any issue please ask us in this Slack channel.

Lesson Slides Hands-on Recordings
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
microgalaxy Nanopore data analysis Pathogens detection Phylogenetic tree Heatmap cyoa