The molecular work was hosted by the Department of Forest Mycology and Plant Pathology at the Swedish University of Agricultural Sciences SLU.
Sequencing was performed by the SNP&SEQ Technology Platform in Uppsala. The facility is part of the National Genomics Infrastructure (NGI) Sweden and Science for Life Laboratory. The SNP&SEQ Platform is also supported by the Swedish Research Council and the Knut and Alice Wallenberg Foundation.
cutadapt v3.10
using default expected error-rate (0.1)DADA2 1.18.0
in R 4.1.3
DADA2
with SILVA 138.1 datasets as reference data (https://doi.org/10.5281/zenodo.4587955), and further assigned to putative species as implemented in the assignSpecies
algorithm, using the same databaseAlignSeqs
algorithm in DECIPHER 2.22.0
phangorn 2.8.1
and likelihood optimized with the optim.pml
functiondecontam 1.14.0
R package (https://doi.org/10.1186/s40168-018-0605-2)
results/contaminant_asvs.txt
intermediate/
- temporary files used throughout the analysis, can be used to modify some steps
phyloseq_object.rds
- saved R object of the assembled phyloseq object after initial processing with dada2metadata/
metadata_vector.txt
- Contains sample information and DNA concentrationsflux_incubated.txt
- Contains flux measurement data in mg-C, expressed per day, per weight and as cumulative valuesdata_description.txt
- Description of data found in Metadata_vector.txt
and flux_incubated.txt
results/
- Final result files
contaminant_asvs.txt
- List of ASVs identified as contaminants (see scripts/contaminants.html)dada2_asvs.fasta
- ASV sequencesanova.manyglm.2k.rds
- saved R object, anova.manyglm object*.pdf
and *.txt
- figures and tables filesscripts/
Manuscript_figures.Rmd
- R notebook of analyses carried out for the manuscript./README.md
- This document