Scorpio Gene-Taxa Benchmark Dataset

We used the Woltka pipeline to compile the complete Basic genome dataset, consisting of 4634 genomes, with each genus represented by a single genome. After downloading all coding sequences (CDS) from the NCBI database, we extracted 8 million distinct CDS, focusing on bacteria and archaea and excluding viruses and fungi due to inadequate gene information. To maintain accuracy, we excluded hypothetical proteins, uncharacterized proteins, and sequences without gene labels. We addressed issues with gene name inconsistencies in NCBI by keeping only genes with more than 1000 samples and ensuring each phylum had at least 350 sequences. This resulted in a curated dataset of 800,318 gene sequences from 497 genes across 2046 genera. We created four datasets to evaluate our model: a training set (Train_set), a test set (Test_set) with different samples but the same genus and gene as the training set, a Taxa_out_set excluding 18 phyla present in the training set but from different phyla, and a Gene_out_set excluding 60 genes from the training set but from the same phyla. We ensured each CDS had only one representation per genome, removing genes with multiple representations within the same species.