Is pre.cluster still necessary for MiSeq data?

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1

Hi,
Considering the lower error rate of MiSeq sequencing compared to 454, why is pre.cluster still a recommended step in the SOP? Why still keep it at 1 difference per 100 bases?

Has anyone actually tested the effect of pre.cluster on a mock community sequenced using MiSeq?

Thanks!
Roey

2

The MiSeq error rate is about the same as we were getting by 454 with shhh.flows. So we do use pre.cluster. See the Kozich paper for data.