Are soft-clipped primer bases included in iVar consensus?

[MonaMe1112]

Hi iVar team,

I’m currently developing a tiled amplicon scheme for HEV (ONT sequencing) and using iVar both for primer trimming and for generating the consensus sequence. So far, this works well for my data.

I have a question about how iVar handles primer-derived bases during consensus generation:

When primers are removed (via iVar primer trimming, resulting in soft-clipped/trimmed primer regions), are those primer bases ever reflected in the final consensus sequence, or are they always excluded from the consensus?

Put differently: does ivar consensus operate strictly on the post-trimming alignments (excluding primer bases), or can primer sequence still influence the consensus at primer-binding sites depending on the workflow/settings?

I will also verify this empirically by comparing consensus sequences generated from primer-trimmed vs. untrimmed alignments, but I’d really appreciate understanding the intended/default behavior in iVar (and whether there are any caveats for ONT data).

Thanks a lot for your help!

Greetings,
Mona

[gkarthik]

Hey Mona, iVar will ignore soft clipped bases including trimmed primers while calling the consensus genome. For ONT data, please keep in mind that you will have to lower quality for both ivar trim and ivar consensus as the default have been set for Illumina data

[MonaMe1112]

Great, that helps a lot ! Also thank you very much for the advice and the fast reply!