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Objects in phyloseq-class format created by following the DADA2 Pipeline Tutorial (Callahan, 2020).
Jeffrey M. Dick, following the DADA2 Pipeline Tutorial by Callahan (2020).
The example dataset for gut communities in a single mouse was taken from the mothur MiSeq SOP. It is an extract of the complete dataset reported by Schloss et al. (2012). The output files were generated by using three different training sets to assign taxonomy to genus level:
mouse.silvasilva_nr99_v138.1: Silva 138.1 prokaryotic SSU taxonomic training data formatted for DADA2
mouse.RDPrdp_train_set_18: RDP taxonomic training data formatted for DADA2 (RDP trainset 18/release 11.5)
mouse.GTDB_220GTDB_bac120_arc53_ssu_r220: DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea (GTDB release 220)
Callahan B (2020). DADA2 Pipeline Tutorial (1.16). https://benjjneb.github.io/dada2/tutorial.html, accessed on 2023-06-14. Publication year taken from https://code.bioconductor.org/browse/dada2/blob/RELEASE_3_11/DESCRIPTION.
Schloss PD, Schubert AM, Zackular JP, Iverson KD, Young VB, Petrosino JF. 2012. Stabilization of the murine gut microbiome following weaning. Gut Microbes 3(4): 383–393. tools:::Rd_expr_doi("10.4161/gmic.21008")
# Load one data set
data(mouse.silva)
# Summarize the object (phyloseq-class)
mouse.silva
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