Genome annotation, comparison and visualization [Galaxy Training]

This dataset provides the input data required to run the Galaxy Training Material tutorial “Genome annotation, comparison and visualization”. The tutorial is partly based on the first steps of the existing Galaxy tutorial “Genome annotation with Funannotate”, which uses the following Zenodo dataset: [1] Anthony Bretaudeau, Alexandre Cormier, Stéphanie Robin, Erwan Corre, & Laura Leroi. (2021). Training data for 'Genome annotation with Funannotate' tutorial (Galaxy Training Material) DatasetData setDataset. Zenodo. https://doi.org/10.5281/zenodo.7867921 From this dataset, the following data are reused: Genome assembly of Mucor mucedo (assembled following the GTN Flye assembly tutorial, then masked with RepeatMasker) [1] RNA-seq reads of Mucor mucedo (SRR8534859 reads mapped to the genome using STAR, then downsampled to reduce the size of the dataset) [1] SwissProt subset provided for functional annotation (subset of SwissProt proteins matching the genome with e-value < 0.0001, as obtained from Diamond) [1] However, unlike the original tutorial, no alternate annotations from the referenced Zenodo dataset are used here. To perform the comparative genomics section (OrthoFinder) and to contrast the Mucor mucedo annotation produced within the tutorial with other species, this dataset additionally includes complete proteomes downloaded from UniProt for several species of the Mucor genus, as well as Saccharomyces cerevisiae used as an outgroup: Mucor ambiguus — UP000053815 Mucor circinelloides — UP000014254 Mucor flavus — UP001473302 Mucor lusitanicus — UP000077051 Mucor plumbeus — UP000650833 Mucor saturninus — UP000603453 Mucor velutinosus — UP001304243 Saccharomyces cerevisiae — UP000002311 These datasets were retrieved directly from the UniProt Proteomes database.