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 ...