Microbial Genomics - computer practical: Glossary

Key Points

Introduction	Z. tritici is an important plant pathogen The genome of Z. tritici is ~40 Mb in size and has core chromosomes and dispensable chromosomes
Genome assembly information	You can obtain assembly information from NCBI You can subset this information and determine the number of genome assemblies
Genome assembly quality	You can compare genome assemblies with quast. You can examine and critically reflect on the impact of genome sequencing technologies on fungal genome assemblies.
Genome assembly completness	You can compare genome completness in eukaryotic genomes with BUSCO. You can critically reflect on the results of BUSCO and provide technical and biological explanations.
Genome comparisons	You can compare two eukaryotic genomes with MUMMER You can critically reflect on the results of MUMMER and provide a technical and biological interpretation of the visual representations. You can combine the learnt methodologies to conceptualise a computational strategy to identify isolate-/species-specific genomic regions.
Introduction to pan-genome graphs	You can generate a pan-genome graph using pggb. You can critically evaluate technical and biological factors that can shape a pan-genome graph.
Genome partitioning	You can determine the similarities between chromosomes. You can critically evaluate a chromosome-network.
Pan-genome graphs of Zymoseptoria tritici	You can build pan-genome graphs for homologous chromosomes. You can critically evaluate the shape of a pan-genome graph and relate it to known biology.

Glossary

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