Code depository associated with: Three thousand five hundred years of sheeppox virus evolution inferred from archaeological and codicological genomes
Year: 2026
Type: article
Abstract: Sheeppox_aDNA Repository containing the analysis pipelines and scripts used in 3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes. Article: Link to article 🧬 Overview This repository gathers all code used for: Screening of sequencing data for Capripoxvirus Mitochondrial analyses and competitive mapping SPPV_ML Phylogenetic analysis of the aSPPV dataset with Pathphynder placement Metagenomic assembly and scaffolding Gene integrity analyses across genomes Pairwise distance calculations and recombination-aware analyses Inactivated genes profiling Phylogenetic dating with BEAST Each directory is a self-contained module or pipeline focused on one part of the analysis. 📁 Repository Structure Screening/Snakemake pipeline for Capripox screening.Includes: Adapter removal Host read removal KrakenUniq-based taxonomic screening Post-pipeline scripts to compute E-values for Capripox viruses. Mitochondrial/Scripts for mitochondrial read mapping and downstream processing.Includes: Mapping to mitochondrial references Scripts to split competitive BAMs into per-species BAM files. SPPV_ML/Phylogenetic analysis of the aSPPV dataset with PathPhynder placement.Includes: Multiple sequence alignments for SPPV genomes ML trees PathPhynder outputs placement Meta_assembly/Post-processing scripts for metagenomic assemblies.Ensures that read pairs are preserved before running SPAdes and RagTag. Gene_integrity/Pipeline for gene integrity analysis across multiple genomes.Works on: A set of genomes in FASTA format A reference GFF annotationProduces summaries of intact vs. disrupted genes. Pairwise_distance/Scripts to compute pairwise genetic distances on Capripox alignments.Features: Pairwise similarity across: The full genome Sliding windows along the genome Option to exclude recombinant regions via an input file Ability to compute distances between species groups using a metadata file. Inactivated_genes_analyses/Multiple sequence alignments of inactivated genes generated with MACSE.Scripts to: Analyze inactivation profiles Summarize patterns of gene disruption. BEAST/All BEAST XML input files used in the paper.Includes: Configured XMLs for different clock / tree models Aligned datasets used as BEAST input.
Authors: L'Hôte, Louis, Sacristán, Luisa, Ferguson, Róisín, Siekmann, Alex, Rogers, Leland, Richter, Barbara, Weissenböck, Herbert, Lorke, Jenny, Artemis, Lara, Lévêque, Élodie, Hark, Richard, Engel, Patricia, Webber, Mary Teresa Josephine, Bennett, Madison, Rose-Beers, Kristine, Nichols, Emma, Munoz Alegre, Marta, Ramsøe, Max, Fiddyment, Sarah, Viñas-Caron, Laura C., Papin, Dimitry V., Light-Maka, Ian C., Key, Felix M., Albarnaz, Jonas, Downing, Tim, Pekar, Jonathan, Lemey, Philippe, Bradley, Daniel, Vnouček, Jiří, Makarewicz, Cheryl A., Story, Joanna, Collins, Matthew, Teasdale, Matthew D., Binois-Roman, Annelise, Calvignac-Spencer, Sébastien, Daly, Kevin G.
Institutions: Trinity College Dublin, University College Dublin, University of East Anglia, University of North Carolina Wilmington, Christian-Albrechts-Universität zu Kiel, University of Veterinary Medicine Vienna, Helmholtz Centre for Infection Research, Courtauld Institute of Art, University of London, Centre National de la Recherche Scientifique, Institut de Recherche et d'Histoire des Textes, Université Paris 1 Panthéon-Sorbonne, Yale University, Universität für Weiterbildung Krems, University of Cambridge, University of Copenhagen, University of York, Altai State University, Siberian Branch of the Russian Academy of Sciences, Institute of Archaeology and Ethnography, Max Planck Institute for Infection Biology, The Pirbright Institute, University of Edinburgh, Rega Institute for Medical Research, KU Leuven, Royal Danish Library, University of Haifa, University of Leicester, University of Oxford, Newcastle University, Archéologies et Sciences de l’Antiquité, Maison des Sciences de l'Homme Mondes, Universität Greifswald
Language: English
Subfield: Virology
Field: Immunology and Microbiology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7204964313