Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2

This repository provides a stable snapshot of TOGA2 data generated for the manuscript listed below. Files assemblies_and_species.tsv provides information about each genome assembly (assembly source, accession, N50s, species names and taxonomy). The tar.gz datasets contain gene annotation, ortholog, and gene loss data produced by TOGA2, which includes- gene annotation with UTRs in bed format (query_annotation.with_utrs.bed)- gene duplication and orthology type information (orthology_classification.tsv)- gene loss data (loss_summary.tsv)- processed pseudogenes and retrogene candidates in bed format (processed_pseudogenes.bed)- genes identified in the query genome in bed format (query_genes.bed). The data is provided as a tar.gz file, one for each TOGA2 reference:reference_chicken_HLgalGal7-GCF_016699485.2reference_cow_HLbosTau10-GCF_002263795.3reference_crow_HLcorHaw3-GCF_020740725.1reference_elephant_HLeleMaxInd3A-GCF_024166365.1reference_emu_HLdroNov3-GCF_036370855.1reference_halibut_HLFhipSten1-GCF_022539355.2reference_human_hg38reference_killifish_HLFnotFurz3-GCF_043380555.1reference_kittiwake_HLrisTri2-GCF_028500815.1reference_mandarinfish_HLFsynSple1-GCF_027744825.2reference_mouse_mm10reference_pondturtle_HLemyOrbi1A-GCF_028017835.1reference_rainbowfish_HLFmelBoes1-GCF_017639745.1reference_riverturtle_HLemyMacqMac1-GCF_026122565.2reference_stickleback_HLFgasAcul3A-GCF_964276395.1reference_zebrafinch_HLtaeGut5-GCF_003957565.2 Unpacking the tar.gz provides subfolders, one per query assembly. The subfolders are named SpeciesName__CommonName__AssemblyName__AssemblyAccession.e.g. Nettapus_auritus__African_pygmy_goose__HLnetAur1__GCA_011076525.1 Additional data, such as softmasked genomes, genome-wide SpliceAI splice site predictions, repeat libraries, whole genome alignments, nucleotide and protein sequences and alignments, and clade-wide sets of 1:1 orthologs are available for download at https://genome.senckenberg.de/download/TOGA2/. For a detailed description of all output files, pls refer to the TOGA2 wiki:https://github.com/hillerlab/TOGA2/wiki Citation If you use the TOGA2 data, please cite: Yury Malovichko et al. "Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2", https://www.biorxiv.org/content/10.64898/2026.06.30.735536v1