Beyond taxonomy: Validating functional inference approaches in the context of fish-farm impact assessments

Project Title

Beyond taxonomy: Validating functional inference approaches in the context of fish-farm impact assessments

Organism

marine metagenome

Organization

Institute of Marine Research

SRA Runs

20

Samples

10

Data

315,229,628 reads, 95.44 Gbp

Description

The aim of this study was to evaluate the performance of three metabolic inference methods, namely PAPRICA, PICRUSt2 and TAX4FUN2, against metagenomics and environmental data, in the context of salmon farm benthic surveys. In particular, we were interested in: 1) comparing predictions and abundance correlations between 16S rRNA amplicon-based metabarcoding functional inference approaches (hereafter referred to as HSP methods) and shotgun metagenomics functional profiling, 2) contrasting the taxonomic and functional microbial diversity recovered from metabarcoding and metagenomics, and 3) assessing and comparing the sensitivity of functional communities derived from HSP methods and metagenomics with respect to microbial turnover and in correlation with environmental data.

inferred primers

Forward

CCTACGGRRBGCASCAGKVRVGAAT

Reverse

TACCAGGGTATCTAATCCT

Samples

10 · primers in 98.9% of reads, median across the assay's samples

11,418 ASVs across the run.

Container image

illumina-amplicon

05f23de10d82

Cluster

grex