- Upload Hafnia fastq data to VIGASP
- Reads_QC: Run basic Reads_QC analysis to check the quality of data and to find if there is any contamination.
- Genome Assembly: Build genome assembly in VIGASP using Assembly and Annotation pipeline
- AMR analysis: Compare against ResPointFinder (VIGASP), MEGARES, CARD and AMRFinderPlus
- Virulence factors: Compare against VirulenceFinder DB
- Phylogenetics:
- Run FastANI to get the basic idea about how the core genome looks like
- CoreGenomeSNP Tree using ALPPACA (https://github.com/NorwegianVeterinaryInstitute/ALPPACA)
- CoreGene Tree using ALPPACA (https://github.com/NorwegianVeterinaryInstitute/ALPPACA)
Folders and files
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