New Illumina i100 system data output question.

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1

Hello,

To give you more context, I do metabarcoding (amplicon 16S, ITS, COI) on environmental samples. Today,
I receive new dataset from Illumina new sequencing system (i100) which uses a new way to call quality per base (Reference: https://knowledge.illumina.com/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009540)

Now, only 4 quality are possible (2,12,24 and 38), so I got a high percentage of my reads that have 38 phred score (G) for every bases. What would be the best course of action to work with these reads. Normally, I use Dada2 to trim and reassemble my forward and reverse read to obtain my amplicon, but since Dada2 need to generate an error model, will it still work correctly when there is almost no quality variation ?

I don’t know if I’m clear enough, I can provide more info if needed.

Thank you in advance.

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2

Hello Pat,

Good news! It's a known issue and Ben is investigating!

The Illumina MiSeq 100 is another one of Illumina's "two-color" instruments: 2-Channel SBS Technology | Faster sequencing and data acquisition

Interesting!

Bad news, there's no fix for DADA2 yet, and once that's working we still need to get this merged into Qiime2. :hourglass_not_done:

Thank you for your patience.

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