OMAnnotator: a novel approach to building an annotated consesus genome sequence

Archive for the associated paper "OMAnnotator: a novel approach to building an annotated consensus genome sequence". This archive contains all sequence data inputs and outputs, sequence processing scripts, analysis scripts and results. Note that paths within scripts will need to be changed to reflect the path to where you download the archive on your machine. OMAnnotator is a tool to combine input annotations from different sources, using evolutionary relationships as a tie-breaker. It involves three steps: data preparation for orthology infernece using the OMAnnotator prepare_data module, orthology inference using the OMA Standalone software, and consensus annotation extraction (based on inferred orthology) using the OMAnnotator extract_consesnus module. Three tar-zipped files are provided: Proof_of_Principle_Dros_Annotations.tar.gz contains all data from the Proof of Principle testing on the Drosophila melanogaster reference. OMAnnotator_Other_Species.tar.gz contains all data from using OMAnnotator to re-annotate three species. 25_species_OMA_Data.tar.gz contains the full OMA Standalone instance for the Proof of Principle run with 25 related species (reported in the main manuscript). Within the Proof_of_Principle_Dros_Annotations.tar.gz and OMAnnotator_Other_Species.tar.gz folders, folders from the orthology inference step (OMA Standalone) of OMAnnotator have the prefix 'Data_OMA', which contain the related species set ('tar.gz' files) downloaded from OMA browser. These related species sets were used to infer orthology in the OMA Standalone step. Thus, these related species files can be unzipped to create an OMA folder and reproduce the OMA Standalone run. See https://github.com/DessimozLab/OMAnnotator for sample slurm scripts to run the OMA Standalone step. For the Proof of Principle run with 25 species (reported in the main manuscript), the full OMA Standalone instance is provided instead (25_species_OMA_Data.tar.gz). The folders OMAnnotator_env.gz and OMAnnotator_Scripts.gz contain the environment and OMAnnotator.py versions used to generate the study results.