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TOGA2

TOGA2 is a revised version of Tool to infer Orthologs from Genome Alignments, which doubles down on the strong points of the original tool while reducing memory and runtime requirements and adding multiple new features.

Warning

TOGA2 is currently in the early access phase. The repository code might undergo minor improvements and bug fixes, and code documentation (cookbook contents, Readme, and this Wiki) will be filled gradually in the following weeks.

Contents

• Installation
• Input files
• Pipeline description
  • Orthology prediction
  • Exon classification
  • Inactivating mutations
  • Loss status classification
  • Query gene inference
  • Ortholog classification
  • Rejection reasons
• Using SpliceAI predictions with TOGA2
• Output description
  • Top level files
  • meta
  • logs
  • tmp
  • nextflow
  • ucsc_browser_files
• Interpreting TOGA2 results
• Logging & troubleshooting
• Glossary