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 ...