R: V4-V5 16S rRNA gene amplicons, clean OTU table (N-ICE, 2015)

nice {ulrb}

R Documentation

V4-V5 16S rRNA gene amplicons, clean OTU table (N-ICE, 2015)

Description

Table in "wide" format with abundance and taxonomic classification of each OTU.

Usage

nice

Format

`nice`

A data frame with 524 rows and 17 columns:

ERR2044662, ERR2044663, ERR2044664, ERR2044665, ERR2044666, ERR2044667, ERR2044668, ERR2044669 and ERR2044670: Sample ID
OTU: OTU ID
Domain: Domain level classification of OTU
Phylum: Phylum level classification of OTU
Class: Class level classification of OTU
Order: Order level classification of OTU
Family: Family level classification of OTU
Genus: Genus level classification of OTU
Species: Species level classification of OTU

...

Details

This OTU table was cleaned so that it only includes samples from 16S rRNA amplicon sequencing and no eukaryotes (similarly to Pascoal et al., 2022). Additionally, we added a column with a ID for each OTU.

For details on raw data, see nice_raw

Source

https://www.ebi.ac.uk/metagenomics/studies/MGYS00001922#analysis

References

Pascoal, F., Costa, R., Assmy, P., Duarte, P., & Magalhães, C. (2022). Exploration of the Types of Rarity in the Arctic Ocean from the Perspective of Multiple Methodologies. Microbial Ecology, 84(1), 59–72. https://doi.org/10.1007/s00248-021-01821-9