Importing clean FASTA files from Illumina

[liubaily]

I get the sequence data in FASTA which has been denoised from the company. How can I use qiime2 to make Feature table and FeatureData?

[jairideout (Jai Ram Rideout)]

Hi @liubaily!

To help answer your question, can you provide these details?

1. Is this 454 or Illumina data?

2. When you say the company has denoised the data, what type of denoising process did they use? For example, denoising may refer to flowgram clustering of 454 data (e.g. as described here), DADA2 (Illumina data), Deblur, or other tools.

Thanks!

[liubaily]

Hi @jairideout,

1. It’s Illumina data.
2. I suppose that they did the denoising process with Qiime1, because they told me that they have demultiplexed the data and chimeric seqs have been removed, and I can begin the analyses of OTU Picking directly with the data in Qiime1. But I want to do this with Qiime 2.

Thank you for your reply!

[jairideout (Jai Ram Rideout)]

Thanks for the details! I’d encourage you to find out exactly what steps were performed by the sequencing center, as that’s important information to keep track of and include in any publications to make your experiment reproducible.

We don’t support OTU picking in QIIME 2 yet – it is tentatively scheduled for the upcoming 2017.9 release (end of this month). We’ll follow up here when it’s available!

In the meantime I recommend processing your data in QIIME 1 (or another tool) and importing the feature table and representative sequences to continue analyses in QIIME 2.

[liubaily]

Thanks for your help @jairideout!

[thermokarst]

QIIME 2 now supports de novo and closed reference OTU picking via vsearch! Yay!