ASV analysis and cluser.fragments

I have been doing OTU-based analysis with no issues but someone in my team has requested that I repeat the analysis using ASVs to compare.

I know that, according to the SOP, pre.cluster is used for this but I have a couple of questions with this. Firstly, I understand that pre.cluster first aligns the sequences. The trouble is, I have a batch of samples that are fungal ITS sequences and I believe it is usually advised that these do not align well. Secondly, I have a limited amount of time to do this (something they have shoehorned in at the last minute) and pre.cluster was taking a long time to run on a sub-set of these unaligned ITS samples, which is to be expected on unaligned sequences.

Given that, I wondered if cluster.fragments would be an acceptable alternative in this situation to perform ASV-based analysis, using the diffs= parameter in the same way as for pre.cluster.

Any advice much appreciated.

Hi PS13 - cluster.fragments should work gtreat for this problem


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