V4-V5 16S rRNA gene amplicons, clean OTU table in tidy/long format (N-ICE, 2015)

Original OTU table (nice) in "long" format.

Usage

nice_tidy

Format

`nice_tidy`

A data frame with 4716 rows and 10 columns:

Sample: Sample ID
Abundance: Abundance
OTU: OTU ID
Domain: Domain level classification of OTU
Phylum: Domain level classification of OTU
Class: Domain level classification of OTU
Order: Domain level classification of OTU
Family: Domain level classification of OTU
Genus: Domain level classification of OTU
Species: Domain level classification of OTU

Source

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

Details

A new column (Sample) includes the sample identifiers and a new column (Abundance) includes the abundance for each OTU. For details on OTU table processing see help pages for nice and nice_raw.

Some details on N-ICE dataset:

This dataset resulted from the Norwegian Young Sea Ice expedition (N-ICE) in 2015 (Granskog et al., 2018). The sample processing and DNA sequencing were described in de Sousa et al., 2019, the bioinformatic processing was performed by the MGnify platform (v5) (Mitchell et al., 2020).

Since the purpose of this dataset if for creating examples and testing the package, we did not apply strict quality control to the final OTU table. Thus, we didn't remove singletons, etc. However, we did remove any non-prokarotic OTUs and organelles, if any (Pascoal et al., 2022).

References

Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., Sakharova, E., Scheremetjew, M., Korobeynikov, A., Shlemov, A., Kunyavskaya, O., Lapidus, A., & Finn, R. D. (2019). MGnify: the microbiome analysis resource in 2020. Nucleic Acids Research, 48(D1), D570–D578.
Granskog, M. A., Fer, I., Rinke, A., & Steen, H. (2018). Atmosphere-Ice-Ocean-Ecosystem Processes in a Thinner Arctic Sea Ice Regime: The Norwegian Young Sea ICE (N-ICE2015) Expedition. Journal of Geophysical Research: Oceans, 123(3), 1586–1594.
de Sousa, A. G. G., Tomasino, M. P., Duarte, P., Fernández-Méndez, M., Assmy, P., Ribeiro, H., Surkont, J., Leite, R. B., Pereira-Leal, J. B., Torgo, L., & Magalhães, C. (2019). Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime. Microbial Ecology, 78(2), 388–408.
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.