Output

Tables

Linelists are collated into a spreadsheet for excel/google sheets:

1. lineage: The recombinant lineages observed.

2. parents: The parental combinations observed.

3. linelist: Results from all input sequences (minimal statistics).

4. summary: Results from all input sequences (all possible statistics, for troubleshooting).

5. positives: Results from sequences classified as a recombinant, as verified by breakpoint detection with sc2rf.

6. false_positives: Results from sequences flagged as recombinants by Nextclade, that were not verified by sc2rf.

7. negatives: Results from sequences classifed as a non-recombinant by nextclade.

8. issues: Metadata of issues related to recombinant lineages posted in the pango-designation repository.

Slides

Powerpoint/google slides with plots embedded for presenting.

Breakpoints

Visualization of breakpoints by parental clade and parental lineage.

Clade	Lineage

Visualization of parental alleles and mutations from sc2rf.