Workflow for long read quality control, contamination filtering, assembly, variant calling and annotation.

• Preprocessing of reference file
• LongReadSum before and after filtering (read quality control)
• Filtlong filter on quality and length
• Flye assembly
• Minimap2 mapping of reads and assembly
• Clair3 variant calling of reads
• Freebayes variant calling of assembly
• Optional Bakta annotation of genomes with no reference
• SnpEff building or downloading of a database
• SnpEff functional ...

Workflow for preprocessing the reference file. Downloads the GenBank file from NCBI if not provided, concatenates plasmid GenBank file(s) with each other and the reference file, extracts GFF3 from the (merged) reference.

This workflow on WorkflowHub: https://workflowhub.eu/workflows/1818

All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/ssb/automated-data-analysis/cwl/-/tree/main/tools Workflows: https://git.wur.nl/ssb/automated-data-analysis/cwl/-/tree/main/workflows ...