SKADI: Sequence-based Knowledgebase for Annotation, Detection, and Identification

SKADI is a simple, homology-based application designed to:

• provide taxonomic annotations for viral contigs

• map reads to virus contigs and support downstream analyses such as tANI/txAAI calculations and visualizations.

Contents

• Installation
  • Installing with conda/mamba
  • Running skadi with singularity
  • Downloading pre-built databases
• Annotating contigs
  • SKADI output
  • Utility workflows
• Annotating reads
• Virus contig annotation pipeline
  • Nucleotide database comparison
  • Protein database comparison
  • Profile database comparison
  • Database Generation Pipeline
• Changelog
  • 0.0.3
  • 0.0.2
• Extras and Citation
  • Helpful command-line snippets
  • Citation

click here to go back to the source code.