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

Steps:

• Preprocessing of reference file : https://workflowhub.eu/workflows/1818
• 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 ...

**Workflow for preprocessing a reference file. **

Steps: -When a GenBank file is not provided, it is downloaded from NCBI based on a accession number. -When multiple plasmid GenBank files are provided, they are merged into one file. -When any amount of plasmid GenBank files are provided, the reference is merged with the plasmid GenBank file(s) into one file. A FASTA file is also extracted. -When no plasmid Genbank files are provided, a FASTA file is extracted from the reference GenBank file. -A ...