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Old 04-30-2017, 07:51 AM   #1
Petr Kozyrev
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Location: Russia

Join Date: Jan 2017
Posts: 2
Default Convert mothur classify.seqs output to BIOM format

I got a lot of problems trying to convert output of mothur classify.seqs to BIOM format so that I can import data into phyloseq R package. I have FASTA file with paired-end reads already being merged with PEAR program.

I aligned my sequences to SILVA database with this command

mothur > align.seqs(fasta=sample.fasta, reference=silva.bacteria.fasta, processors=4, flip=t)

and then I classified it using the same database

mothur > classify.seqs(fasta=sample.align, reference=silva.bacteria.fasta,, cutoff=80)

After this procedure I got different files: "sample.summary", "" and "". But I don't know how to import them into phyloseq R package.

I've read here about shared file from which I can create BIOM file, but I don't have .list or .group files for make.shared command.

Can someone help?

Sincerely yours,


Last edited by Petr Kozyrev; 04-30-2017 at 08:09 AM.
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Old 05-01-2017, 06:37 AM   #2
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Location: CT

Join Date: Apr 2015
Posts: 242

You have only classified your sequences, you haven't clustered them into OTUs which generates your list and shared files. Have you tried following the mothur how to?
Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
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Old 05-01-2017, 09:46 AM   #3
Petr Kozyrev
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Location: Russia

Join Date: Jan 2017
Posts: 2

Thank you for your quick response!

I didn't mention that I used RDPTools classifier for my purposes earlier, but then some samples were classified badly. So I decided to check, if RDPTools classifier is not very good, and try mothur classifier. To achieve my goal I wanted to omit some steps in mothur SOP so that I can compare only classifiers in both pipelines. But now I realize it wasn't a really good idea.

I'll try to follow this SOP step by step now.

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mothur, phyloseq

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