16S data analysis from minION with QIIME?

[manojndsu (Manoj Kumar)]

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

Thanks

[colinbrislawn (Colin J Brislawn)]

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!

GitHub - MaestSi/MetONTIIME: A Meta-barcoding pipeline for analysing ONT data...

GitHub - DeniRibicic/q2ONT: Bash pipeline for analysis of ONT full-length 16S...

You could try using one of those!

Colin

[manojndsu (Manoj Kumar)]

Thank you for letting me know.

[manojndsu (Manoj Kumar)]

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)

[colinbrislawn (Colin J Brislawn)]

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

[manojndsu (Manoj Kumar)]

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.

[Nicholas_Bokulich]

@manojndsu

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

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!

[MaestSi (Simone Maestri)]

@Nicholas_Bokulich

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

[manojndsu (Manoj Kumar)]

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

[MaestSi (Simone Maestri)]

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