Performance Testing of Fungal Proteomes

We constructed sets of fungal proteomes of increasing size for performance testing. Ensembl Genomes was interrogated on 6 November 2017 using its REST API [44 (link)] to identify all available fungal genomes. To achieve an even sampling of species, we selected 1 species per genera and excluded genomes from candidate phyla or phyla with fewer than 3 sequenced genomes. This gave a set of 272 species which were downloaded from the Ensembl FTP site [45 (link)]. We created datasets of increasing size by randomly selecting 4, 8, 16, 32, 64, 128, and 256 species such that the last common ancestor was the same for each dataset. Each dataset was analyzed using a single Intel E5-2640v3 Haswell node (16 cores) on the Oxford University ARCUS-B server using 16 parallel threads for OrthoFinder with DIAMOND (arguments: “-S diamond -t 16 -a 16”). The complete datasets for all analyzed species subsets are available for download from Zenodo at 10.5281/zenodo.1481147. All methods submitted to Quest for Orthologs that provided a user-runnable implementation of the method were tested on the same fungi datasets and the same ARCUS-B server nodes and run in parallel using 16 threads (when supported by the method).