Workflow for quality assessment and taxonomic classification of amplicon long read sequences. In addition files are exported to their respective subfolders for easier data management in a later stage.

Inputs are expected to be basecalled fastq files

Steps:

• NanoPlot read quality control, before and after filtering
• fastplong read quality and length filtering
• Emu abundance; species-level taxonomic abundance for full-length 16S read

Assembly and intrahost/low-frequency variant calling for viral samples