Can Ion Torrent sequencing data be analyzed in QIIME2

[Brandon]

Hi, community,

I have looked through the forum on Ion Torrent sequencing data analysis. However, some said it can while some said not. So I am confusing. Can DADA2 or DEBLUR analyze Ion Torrent sequencing data? Can DEBLUR be safe in the analysis?

Thanks in advance.

[colinbrislawn (Colin J Brislawn)]

Hello Brandon,

You have probably already found these posts, but I wanted to say that while there is not a tutorial, yes, you can import Ion Torrent Data into Qiime 2.
link
link
link

You can start by importing your data using the fastq manifest format.

If you have any questions, feel free to look for clues in those three other threads, or post your questions here!

Colin

[Brandon]

Hi, @colinbrislawn,

Thanks so much. How about Hiseq data? The same ways around?

[colinbrislawn (Colin J Brislawn)]

Hello Brandon,

For the Illumina HiSeq? Sure. If anything, that should be more similar to the MiSeq data shown in the tutorials. And as long are your different samples are in different files, you can use the fastq manifest format with either

--type 'SampleData[SequencesWithQuality]'
or
--type 'SampleData[PairedEndSequencesWithQuality]'

Let me know how well this works for you. More tutorials need to be written to handle different kinds of data, so your feedback helps us know where to focus next.

And if something is broken, let us know so we can fix it!

Colin

[Brandon]

Hi, @colinbrislawn,

Thanks so much for the answer. I will do that and give the feedbacks.

[ebolyen (Evan Bolyen)]

Hi @Brandon,

Jumping in real quick to answer this particular question:

@Brandon

Can DADA2 or DEBLUR analyze Ion Torrent sequencing data? Can DEBLUR be safe in the analysis?

My current understanding is that Deblur hasn't been validated for Ion Torrent yet, and the current recommendation for DADA2 and Ion Torrent is to set your trim-left parameter to 15 (or more).

I honestly don't expect Deblur to have issues with that data, but you should probably make sure that what you see makes sense (by comparing it to DADA2 for example).

[Brandon]

Hi, @ebolyen,

Thanks so much for your response. I see. I am under try.