Habitat and tree species identity shape aboveground and belowground fungal communities in Central European forests
This repository contains the data and pre-processing pipeline, as well as the R script for the analysis accompanying our paper:
Hofmann B, Dreyling L, Dal Grande F, Otte J & Schmitt I 2023. Habitat and tree species identity shape aboveground and belowground fungal communities in Central European forests. Frontiers in Microbiology doi: 10.3389/fmicb.2023.1067906.
Lukas Dreyling
Doctoral Candidate
E-Mail
Imke Schmitt
Principal Investigator
E-Mail
Francesco Dal Grande
Principal Investigator
E-Mail
Additionally you need to download the raw reads here.
If you lack the computing power to process the raw reads, the resulting ASV tables, FASTA files, taxonomy table and metadata are located here.
An archived version of this repository can be found at Zenodo.
- fastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- Cutadapt https://cutadapt.readthedocs.io/
- R https://www.r-project.org/
- BLASTn https://www.ncbi.nlm.nih.gov/books/NBK279690/
- R https://www.r-project.org/
- Rstudio https://www.rstudio.com/
- here https://here.r-lib.org/
- tidyverse https://www.tidyverse.org/
- decontam https://benjjneb.github.io/decontam/
- phyloseq https://joey711.github.io/phyloseq/
- LULU https://github.com/tobiasgf/lulu
- Biostrings https://bioconductor.org/packages/release/bioc/html/Biostrings.html
- microbiome https://github.com/microbiome/microbiome
- fantaxtic https://github.com/gmteunisse/Fantaxtic
- igraph https://igraph.org/
- SpiecEasi https://github.com/zdk123/SpiecEasi
- ranacapa https://github.com/gauravsk/ranacapa
- rgexf https://github.com/gvegayon/rgexf
- vegan https://rdrr.io/cran/vegan/man/vegan-package.html
- MicEco https://github.com/Russel88/MicEco