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).