Path: blob/main/learning-pathways/bacterial-comparative-genomics.md
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---layout: learning-pathway title: Bacterial comparative genomics description: | This learning path aims to teach you how to analyze bacterial genomes, starting with genome retrieval from NCBI and GTDB. The workflow will include quality control (CheckM2), dereplication (dRep), and pangenomic analysis (PPanGolin). Functional and structural annotation will be performed, with a focus on identifying mobile genetic elements and antimicrobial resistance genes. Phylogenetic analysis will compare core genome trees and presence-absence pangenome trees to reveal complementary evolutionary insights. draft: true type: use tags: [bacteria, comparative genomics, pangenome, phylogeny, microgalaxy] editorial_board: - bebatut funding: - ifb pathway: - section: "Module: Dataset construction" description: | For comparative genomics, dataset construction is the first essential step. Here we explain how to build a dataset mixing public and private genomes or assemblies. tutorials: - name: bacterial-comparative-genomics-dataset-construction topic: genome-annotation - section: "Module: Genome quality control" description: | Before genome comparison, quality of genomes and assemblies needs to be checked. tutorials: - name: bacterial-genome-quality-control topic: genome-annotation - section: "Module: Structural and functional annotation" description: | Genomes and assemblies must can be annotated to detect genes with a focus on identifying mobile genetic elements and antimicrobial resistance genes. tutorials: - name: bacterial-genome-annotation topic: genome-annotation - name: amr-gene-detection topic: genome-annotation - section: "Module: Pangenomic analysis" description: | Genomes and assemblies must can be annotated to detect genes with a focus on identifying mobile genetic elements and antimicrobial resistance genes. tutorials: - name: bacterial-pangenomics topic: genome-annotation - section: "Module: Phylogenetic analysis" description: | Phylogenetic analysis allows visualization and compares core genome trees and presence-absence pangenome trees to reveal complementary evolutionary insights tutorials: - name: bacterial-comparative-genomics topic: evolution
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