PUB - Publikationen an der Universität Bielefeld

# Test set for QUOD (Reference-based QUantification Of gene Dispensability) ## Background: Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in (almost) all investigated individual genomes, and dispensable genes, which only occur in a single or a few investigated genomes. The binary classification as ‘core’ or ‘dispensable’ is often based on arbitrary cutoffs of presence/absence in the analysed genomes. Instead of classifying a gene as core or dispensable, QUOD assigns a dispensability score to each gene. Hence, QUOD facilitates the identification of candidate dispensable genes which often underlie lineage-specific adaptation to varying environmental conditions. ## Test set: The test dataset for QUOD comprises genomic reads of four randomly selected accessions of the *Arabidopsis thaliana* Nordborg set. The reads were retrieved from the Sequence Read Archive (SRA) and mapped against the AthNd1_v2c reference genome sequence [1] using bowtie2 [2]. To reduce the size of the files, the first Mbp of Chr1 was extracted. All BAM files provided here are already sorted and should be used as input for QUOD which is available on GitHub: https://github.com/ksielemann/QUOD. A dispensability score is calculated for each gene. Optionally, the results can be visualized as a colored histogram and a box plot.

##### References: _{[1] Pucker B, et al. A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PloS one 14.5 (2019): e0216233. [2] Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.}