cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and traceback based on NCBI Pathogen Detection Project for Cronobacter.
This is the first release of the data analysis pipelines. It:
- Performs read quality filtering using
fastp. - Performs de novo assembly using
shovill. - Performs genome assembly polish using
polypolish. - Performs gene prediction and annotation using
prokka. - Generates assembly metrics using
quast.py. - Subtypes assemblies using
RMLST. - Performs whole genome based comparison using
mashandmashtreeusing NCBI Pathogen Detection for Cronobacter. - Optionally performs pangenome analyses using
pirate.