chem16S (version 1.2.0)

chem16S-data: `phyloseq-class` objects generated using the DADA2 Pipeline Tutorial

Description

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

Author

Jeffrey M. Dick, following the DADA2 Pipeline Tutorial by 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_220

GTDB_bac120_arc53_ssu_r220: DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea (GTDB release 220)

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. tools:::Rd_expr_doi("10.4161/gmic.21008")

Examples

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