ASV vs OTU for fungal ITS

[salias (Sergio Alías-Segura)]

Hi there!

@Saptarathi_Deb

After going through many publications I am seeing comments against the use of ASV for fungal ITS

I'm really curious about that. Could you share the publication reference(s)?

@Saptarathi_Deb

1. ITS is variable in length and not suitable

I don't see why that should be a problem when creating ASVs with e.g. DADA2. But maybe I'm too naive to understand the implications.

@Saptarathi_Deb

2. Fungal ITS show intraspecific and intragenomic differences and thus ASV ITS sequences must be clustered to approach species level resolution.

I understand the point, but I don't think OTUs would be better than ASVs in this case. If a species has several ITS sequences, once you assign taxonomy you can either:

• Report ASVs individually like "ASV belonging to species X".
• Collapse (cluster) by any taxonomic level (in this case, species), so you can work with grouped ASVs for each species.

Personally I would stick to ASVs for ITS analyses. In fact, that's what I'm doing right now. But I'm open to change my mind if the reasons are big.

Best,

Sergio

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