cronology v0.2.0

cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and traceback based on NCBI Pathogen Detection Project for Cronobacter.

New in v0.2.0:

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Features:

• The pipeline now automatically uploads the mashtree generated output along with metadata to microreact.org. Please refer to the instructions on how to take advantage of this feature.

Bug fixes:

• Fixed a bug with the QUAST module which had incorrect container URL and incorrect software version generator.
• Fixed a bug wherein rMLST fails gracefully if the contigs file size is greater than 10 MB.
• Fixed a bug where in DOWNLOAD_REF_GENOME module was failing with docker container.
• Other QoL fixes. 

cronology v0.1.0

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 mash and mashtree using NCBI Pathogen Detection for Cronobacter.
• Optionally performs pangenome analyses using pirate.