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DADA2 vs Deblur urchin Bioinformatics 1 05-28-2018 06:36 PM

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Old 01-16-2018, 12:23 AM   #1
sda89
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Default DADA2 vs Deblur

Hi all!!

I'm a PhD student working on microbiome and mycobiome in skin dog!

I'm learning how to analyse bacterial sequences from IonTorrent, using the QIIME2 program. I saw in the tutorial of QIIME2 that is possible to apply DADA2 or DEBLUR for the analysis.

My question is: what do you think about DADA2 and DEBLUR? which one would be recommended to obtain good results?

Thank in advance!!

best regards

Sara
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Old 01-16-2018, 07:52 AM   #2
thermophile
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Why IonTorrent? MiSeq is cheaper and much better sequence quality for amplicons? Besides dada2 and deblur are both for illumina sequencing, applying them to IonTorrent would require quite a bit of groundtruthing that I don't think has been done (I'm sure someone will jump in with references if I'm wrong on this).
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Old 01-17-2018, 03:58 AM   #3
Bukowski
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'Deblur has not been evaluated with Ion Torrent': https://forum.qiime2.org/t/deblur-p-...failure/1880/5

DADA2 recommendations for Ion Torrent data: https://github.com/benjjneb/dada2/issues/67

This may guide your choice.
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Old 01-17-2018, 04:22 AM   #4
sda89
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Dear Thermophile and Bukowski,

Really thank for replying me! We only have IonTorrent for sequencing, so that's the reason why I was asking if it would be good to analyse sequences with DADA2 or Deblur.
I know that both are for Illumina, but I saw in QIIME2 tutorial and on QIIME2 forum that they can be used for IonTorrent too. As I'm not an expert of DADA2 and Deblur, I asked an advice!!

Thank you again!!


Sara
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Old 01-18-2018, 11:14 AM   #5
snetmcom
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The other option is to use Ion Torrent's microbial pipeline. I have not used it, but I know a group that exclusively uses it for their metagenomic workflow.
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Old 04-22-2018, 01:46 AM   #6
isalarubi
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Quote:
Originally Posted by snetmcom View Post
The other option is to use Ion Torrent's microbial pipeline. I have not used it, but I know a group that exclusively uses it for their metagenomic workflow.
Dear @sentmcom,
could you put me in contact with the this group using the Ion torrent pipeline? I have tried to use it, but although the accuracy of the prediction is really good, it has a lot of limitations to work on it, and I am looking for somebody that uses it to interchange information.
Thanks in advance
Isabel
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