16S microbiome analysis using QIIME2 and PacBio long reads

[Nandan_Deshpande]

Hi,

I wanted to use QIIME2 for my 16S microbiome analysis using PacBio long reads (v3 SMRT cell).

When I searched for ways to import 16S long read data into QIIME2, I found a previous discussion which said that workaround was to analyse the data 'directly with dada2 using R' and then possibly import it in QIIME2?

importing fasta file from PacBio

Good morning @binzuo Welcome to the forums! I have some bad news for you; long PacBio reads are supported by dada2 1.10, but they are not yet supported by the Qiime2 plugin. But we are working on it! You can keep track of our progress here: For now, you would have to process your data directly with dada2 using R. Colin

I wanted to check if there is any further development on this front and if there is a more streamlined approach for this analysis?

Thanks in advance,

Nandan

[Keegan-Evans]

@Nandan_Deshpande,

It looks like we are reviewing a PR that adds this functionality for the QIIME2 2021.8 release that is coming at the end of the month! Feel free to take a look at it here.

[Nandan_Deshpande]

Great thanks Keegan-Evans

Is there a way I can use the code earlier ?
I am trying to get to run DADA2 in R at this time and then continue with Qiime2.

An alternate approach within Qiime2 should work great !

If not I will wait. Thanks for your help,

Nandan

[Keegan-Evans]

@Nandan_Deshpande,

It is BSD 3-Clause Licensed, so you are welcome to pull down the code(from the link that I sent before) and use it at any point point under the stated terms and conditions. That being said, we will not be offering support on it until the official release. As it is not part of the release yet, you would have to approach it more like a developer so you might want to check out our dev docs page. We are only about 2 weeks out from the release now so it might be worth just waiting until then.

[Nandan_Deshpande]

Thanks @Keegan-Evans

Appreciate your feedback,

regards,

Nandan

[Keegan-Evans]

@Nandan_Deshpande,

Of course! This topic is definitely one that has generated a lot of interest.

I will note that while this PR is in the 'Under Review' section of the new release, there is no guarantee that it will be included with the new release. If it is not included, you are still welcome to use it, though as previously stated we would not be offering official support for it yet. If that ends up being the case, the original PR author may or may not be able to answer any questions.

Hopefully that will not end up being the case but there is always the possibility that some issue(such as a conflict during the build for the release) may come up which prevents it from being included.

[Nandan_Deshpande]

Thanks Keegan-Evans.

Fingers crossed.

Cheers,

Nandan