DADA2 analysis for two different platforms MISEQ and Novaseq -Merging of sequence table

[Jayakanthankk]

I have sequenced V3V4 region 50 samples in each by two platforms MISEQ and Novaseq and two different formats 2x250 and 2x300 bp. Is possible to merge sequences from both runs and construct sequence tables, followed by assigning taxonomy. Basically all samples of same cohort. How to analyses and what codes required for this.

[benjjneb]

Yes, as long as the primer sets you are using are the same you can simply merge ASVs across those sequencing types.