Does synteny cause issues for middle-quality MAGs?

[HongyuDD]

Hi,

Thank you for this amazing tool! I am using Panaroo to build genus-level pangenomes on MAGs with the following quality:

• completeness >70%
• contamination <10%

I understand that Panaroo performs gene fragment correction based on synteny. But for MAGs of this quality, synteny may not always be reliable. I am wondering whether the synteny could affect the accuracy of the pangenome in this case?

Many thanks!

[gtonkinhill]

Hi,

Yes, unreliable gene synteny is likely to reduce the accuracy of the pangenome. We are working on methods to make Panaroo more robust to diverse datasets like this but these are still in the early stages.

For the moment, it's probably best to run Panaroo in it's 'sensitive' mode to prevent real genes from being filtered out by Panaroo's error correction steps. You could also look at reducing the clustering thresholds for the initial gene clustering step. By default --threshold is set at 0.98, so I would probably reduce this to at least 0.95 or even lower in your case.

If you have multiple genomes of the same species. You could also look at first building species level pangenomes and then merging them together using the panaroo-merge function. This would improve the error correction at the species level.