ncov-recombinant

Reproducible workflow for SARS-CoV-2 recombinant sequence detection.

1. Align sequences and perform clade/lineage assignments with Nextclade.

2. Identify parental clades and plot recombination breakpoints with sc2rf.

3. Create tables, plots, and powerpoint slides for reporting.

Table of Contents

• What is recombination?
  • Pipeline Definition
  • Designated Recombinants
  • Novel Recombinants
• Install
• Update
• Tutorial
• Output
  • Tables
  • Slides
  • Breakpoints
• Controls
  • Genbank
  • GISAID
• Configuration
• High Performance Computing
• Developer’s Guide
  • Trigger 1 | New Lineage Dataset
  • Trigger 2 | New Nextclade CLI
  • Trigger 3 | New Proposed Lineage
  • Trigger 4 | New Designated Lineage
  • Validation
• FAQ
• Credits

Indices and Tables

• Index

• Module Index

• Search Page