Paired end, dada2 takes a long time to run, alternative ways?

[zwei (Zhengzheng Wei)]

Wondering if there are alternative ways to denoise other than dada2 for paired end data.

Can paired end data be joined in Qiime2 and denoised with deblur? if yes, what to use for join paired end data?

can Qiime2 qza file be exported and using a thired-party software/script to denoise and import back to Qiime2 for downstream analysis?

Thanks,

[jairideout (Jai Ram Rideout)]

Hi @zwei!

@zwei

Wondering if there are alternative ways to denoise other than dada2 for paired end data.

Your topic title indicates that DADA2 is taking a long time to run. Have you tried running it in parallel by supplying --p-n-threads to dada2 denoise-paired?

@zwei

Can paired end data be joined in Qiime2 and denoised with deblur? if yes, what to use for join paired end data?

Deblur (available in q2-deblur) and vsearch (available in q2-vsearch) both work with joined sequences, but we unfortunately don't have a read-joining plugin yet in QIIME 2. You'll need to join your reads with an external tool, or by using QIIME 1's join_paired_ends.py script. After joining your reads, you can import them as single-end data and process with Deblur or vsearch.

We'll follow up here when there is a read-joining plugin available in QIIME 2!

@zwei

can Qiime2 qza file be exported and using a thired-party software/script to denoise and import back to Qiime2 for downstream analysis?

Yes! See the exporting tutorial and importing tutorial for examples.

[zwei (Zhengzheng Wei)]

thanks, very helpful, will give it a try.

[jairideout (Jai Ram Rideout)]

The QIIME 2 2017.11 release has expanded support for analyzing paired end reads! See the paired end reads community tutorial for more details.