Hello everyone,
I am running a simple denoising DADA2 pipeline for a panel of amplicon(s). I got the same samples but sequenced with different platform i.e. Aviti and Illumina. I am curious about their technical replicate concordance rate because afterwards I merge the replicates.
Aviti has consistently lower concordance (54% in this case) than Illumina (74%). I would like to know if this is the expected behavior OR is it recommended to adjust the params of DADA2 accordingly for each sequencing tech?
I am using these parameters for DADA2:
- "maxEE": "5,5",
- "trimRight": "0,0",
- "minLen": 30,
- "truncQ": "5,5",
- "max_consist": 10,
- "omegaA": 1e-120,
- "matchIDs": 1,
- "justConcatenate": 0,
- "saveRdata":"",
- "qvalue": 5,
- "length": 20
The reason I got curious about this is that my main dataset sequenced via AVITI has a concordance rate of just 15%.
Thank you for any input/solution/guidance! :-)
More info>
Aviti_errF
Aviti_errR
Illumina_errF
Illumina_errR
Main Aviti Dataset errF
Main Aviti Dataset errR
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So every sample library has been sequenced on both platforms? I am not familiar with Aviti but does it require any additional mods or can the Illumina libraries be used as is. If the answer is yes, you may have a uniqe dataset that not many are likely to have.
Can you explain what do you exactly mean by concordance? Is the number of cycles of sequencing identical on both platforms?