Use	Tools	References
Quality Control	FastQC, MultiQC	(Andrews, 2010; Ewels et al., 2016)
Primer/adapter trimming	Cutadapt, Trimmomatic	(Bolger et al., 2014; Martin, 2011)
Amplicon denoising	DADA2, Deblur, UNOISE2	(Amir et al., 2017; Callahan et al., 2019; Edgar, 2016)
Taxonomy databases	RDP, SILVA, Greengenes	(Cole et al., 2013; DeSantis et al., 2006; Quast et al., 2012)
Phylogeny	FastTree	(Price et al., 2010)
Analysis suites	QIIME2, mothur, phyloseq	(Bolyen et al., 2019; McMurdie and Holmes, 2013; Schloss et al., 2009)
Pipelines	IMNGS, nf-core/ampliseq	(Lagkouvardos et al., 2016; Straub et al., 2020)
Differential abundance	ALDEx2, ANCOM/ANCOM-BC, DESeq2, gneiss, LEfSe, MaAsLin2, selbal	(Fernandes et al., 2014; Lin and Peddada, 2020b; Love et al., 2014; Mallick et al., 2021; Mandal et al., 2015; Morton et al., 2017; Rivera-Pinto et al., 2018; Segata et al., 2011)
Machine learning	mikropml, SIAMCAT	(Topçuoğlu et al., 2021; Wirbel et al., 2021)
Data repositories	ENA/SRA	(Leinonen et al., 2011)
Tools for reproducible research	GitHub/GitLab, Rmarkdown, Jupyter notebooks	(Allaire et al., 2021; Kluyver et al., 2016)