16S data analysis from minION with QIIME?

Hi,
I have 16S microbiome data from minION to analysis. Please share a workflow to analyse these sequences using QIIME2 pipeline.

Thanks

Hello Manoj,

Welcome to the forums! :qiime2:

Unfortunately, there is not an ‘official’ tutorial on using ONT minION reads inside Qiime 2, but people have been making their own pipelines!


You could try using one of those!

Colin

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Thank you for letting me know.

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Hi, I have a excel file (attached) of MinION data, I need to identify classification of bacteria from the taxid. Please suggest how to run QIIME2 with these type of data or I must have sequence to run QIIME.

Thanks!
data.csv (632 Bytes)

Unfortunately, you will need sequences inside of the fastq files for analysis.

Find the fastq file (or fast5 files) and then you can start using Qiime 2!

Colin

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Hi,
I am not getting file “sample_name”_taxonomy.qza" with the command.
./Import_database.sh sequence.fasta

##############


I am getting following error, please see attachment.

This is not a QIIME 2 action. I am guessing that you are using one of the external pipelines that @colinbrislawn recommended? If so, you should follow the support directions associated with that pipeline — these are not developed by the QIIME 2 team and so we (the moderators on this forum) don’t know how to troubleshoot your issue.

Though if @MaestSi or @Deni_Ribicic wish to provide support for their QIIME 2 minION pipelines through this forum they are welcome to!

Hi,
the described issue involves installation and configuration of MetONTIIME pipeline. I am providing support through the GitHub Issues tracker, where @manojndsu just posted.
Thanks,
Simone

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Hi, I am new with this platform, please let me know if I can use QIIME 2 for my MinION data.

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It took some time for pipeline configuration, possibly due to conflicts between anaconda and miniconda installations, but @manojndsu has eventually accomplished taxonomic classification of his samples.
Simone

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