'phyloseq-class' objects generated using the DADA2 Pipeline Tutorial

Description

Objects in phyloseq-class format created by following the DADA2 Pipeline Tutorial (Callahan, 2020).

Details

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.silva’

silva_nr99_v138.1: Silva 138.1 prokaryotic SSU taxonomic training data formatted for DADA2

‘mouse.RDP’

rdp_train_set_18: RDP taxonomic training data formatted for DADA2 (RDP trainset 18/release 11.5)

‘mouse.GTDB_214’

GTDB_bac120_arc53_ssu_r214: GTDB: DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea

Author(s)

Jeffrey M. Dick, following the DADA2 Pipeline Tutorial by Callahan (2020).

References

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. doi:10.4161/gmic.21008

Examples

# Load one data set
data(mouse.silva)
# Summarize the object (phyloseq-class)
mouse.silva