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. Start with the tutorial at your own pace. If you need support contact us via the Slack Channel #gta_bacterial_genomics.

Organiser(s)
orcid logoBérénice Batut avatar Bérénice Batutorcid logoClea Siguret avatar Clea Siguret
Instructor(s)
orcid logoAnna Syme avatar Anna Symeorcid logoBérénice Batut avatar Bérénice Batutorcid logoClea Siguret avatar Clea Siguretorcid logoEngy Nasr avatar Engy NasrGareth Price avatar Gareth PriceIgor Makunin avatar Igor MakuninMeltem Kutnu avatar Meltem Kutnuorcid logoPaul Zierep avatar Paul Ziereporcid logoSaim Momin avatar Saim Momin

Need help with these tutorials?

Open Slack support channel for this track:   #gta_bacterial_genomics

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