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  • 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

  • #2
    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).
    Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

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    • #3
      '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.

      Comment


      • #4
        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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        • #5
          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.

          Comment


          • #6
            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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