Code depository associated with: Three thousand five hundred years of sheeppox virus evolution inferred from archaeological and codicological genomes

Résumé fourni par la source

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.

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