TABLE 1.

Overview of the AcetoScan analysis process.

Step	Process	Task	Dependency
1	Quality control	Primer sequence trimming and quality filtering	Cutadapt (Martin, 2017)
2	Sequence data analysis	Dereplication, denoising, chimera removal, clustering, OTU picking	VSEARCH (Rognes et al., 2016)
		Filtering non-target sequences and best frame analysis	Bioperl (Stajich et al., 2002), NCBI-blast+ (Camacho et al., 2009), AcetoBase (Singh et al., 2019)
		OTU table generation and taxonomic assignment	NCBI-blast+, VSEARCH, AcetoBase
3	Phylogenetic inference	Multiple sequence alignment	MAFFT (Katoh and Standley, 2013)
		Phylogenetic tree computation	Fasttree (Price et al., 2009)
4	Visualization	Plotting various plots for taxonomic abundance, alpha and beta diversity graphs, phylogenetic tree visualization	R and dependencies (R Core Team, 2011)