2.2.5 vAMPirus Analyze pipeline and report
The Analyze pipeline includes multiple analyses (e.g., phylogenetics, taxonomy inference); results are summarized in a final HTML report with tables and interactive figures (Supplemental Figure S3). The pipeline also organizes and stores output (e.g., counts tables, similarity matrices, taxonomy files) from these analyses within a user-specified results directory. Integration into Nextflow allows different analytical approaches (e.g., ASV grouping approach) to be run in parallel. Primary processes and analyses are summarized below; additional processes, such as percent similarity matrix generation and protein physiochemical property analyses are reviewed in the supplemental materials (Section S1).