How to generate ASVs on on from Mothur tutorial on galaxy -- Resolved, OTU == ASV

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#1

have been working through the 16S microbial analysis with mothur using my data. I have followed the tutorial on galaxy.eu. I was hoping to generate an ASV file instead of an OTU, and I was wondering how I could do that? I ran the pre.cluster tool, followed by removing chimeras and lineages. I used the make.shared tool but it required a list file that I do not have. I also tried to cluster tools to generate a list file but that only resulted in an error. How do I generate an asv table from the make.shared tool if I do not have a list file.

I am new to Bioinformatic and I am sorry to have to bother you with such questions.

I hope to hear from you soon.

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#2

A rose by any other name… Someone can correct me if I’m wrong here, but I believe you can simply rename your OTUs as ASVs. I think the change is not really about methodology, but about the concept of an OTU, and why it should be renamed as ASV. Here is Benjamin Callahan’s paper on it.

I have found a little misinformation out there about this, including on the Zymo website, which indicates that another acceptable term is ESV – But do not use the phrase ESV. Callahan himself regrets accidentally introducing the term ESV into the literature. Here you can see he said

“I also want to apologize for accidentally introducing another alternative into the literature. When we changed from SV to ASV in our paper, we didn’t change the title ‘Exact sequence variants should replace operational taxonomic units in marker-gene data analysis’, and I suspect we are responsible for ‘ESV’ now popping up in a number of places. Sorry!”

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