VGO3 upper airway microbiome in pneumonia datasets

This dataset contains two ready-to-use R phyloseq objects representing upper airway microbiota profiles, provided in both raw (ps_lim_raw.Rds) and pre-processed (ps_lim_cleaned.Rds) formats. Data accompanies the manuscript 'Upper airway microbiota in individuals with community-acquired pneumonia: A case-control study in rural general practice patients'. How to cite this material: 10.5281/zenodo.16458052. The phyloseq objects contains three component ASV table: Counts of amplicon sequence variants (ASVs) per sample. Taxonomic table: Taxonomic classification for each ASV (e.g., kingdom to species level). Sample metadata: Minimal sample-level information Further metadata can be provided upon reasonable request. The pre-processed data can be used as input for the scripts on GitLab. Using an in-house bioinformatics pipeline, paired-end reads were processed with DADA2 (v1.16.0; maxEE = 2; truncLen = 200/150) to infer amplicon sequence variants (ASVs). Chimeras were detected and removed using the 'consensus' method. Taxonomy was assigned using the naïve Bayesian classifier with the Silva v138 (Version 2; August 2020) reference database. All other DADA2 parameters were set to their default values.