How to build an OTU table using ONT sequencing

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1

Hi,

I received my 16S sequences already demultiplexed, and we used Oxford Nanopore on the MinION platform.

I’m trying to build my OTU tables to continue with my analysis, but I’m not sure if I’m doing it correctly because most tutorials I’ve found are for Illumina sequences. I have already imported my data, and I’m trying to run the following command to obtain the otu clustering:

qiime vsearch dereplicate-sequences
--i-sequences demux.qza
--o-dereplicated-table table.qza
--o-dereplicated-sequences rep_seqs.qza

But I’m not sure how to proceed after that, if I aready have my OTU table with it or what can I do to obtain it. Are there any tutorials or resources available that could help me with this?

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7

Hi @ana_btt, Have you reviewed this post yet:

That might help you get started. Additionally there are some ONT-focused plugins on the horizon, but nothing in the distros or on the QIIME 2 Library yet.

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8

Hi, thank you for replying to me. I hadn't seen this post yet, but I just checked it out and I think it will be very helpful.

Thank you again!

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9

Hi Ana,

I hope you’ll find PRONAME useful.
If you need any support, feel free to open an issue on GitHub.

Cheers,
Ben

2 Likes
10

Hi there,

another option for you worth considering is PIMENTA: GitHub - WFSRDataScience/PIMENTA: PIMENTA for rapid identification of species using MinION sequencing

chs

Marcel

1 Like
11

Hi Marcel,

Thank you for replying to me, definitely I will check this option as well.

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