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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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Nanopore variable region sequencing analysis #1364

Open CarlaCristinaUranga opened 3 years ago

CarlaCristinaUranga commented 3 years ago

Hi,

I have Nanopore sequencing data for the 16s gene of microbioal communities. Can dada2 be used for this type of sequencing data, and if not, is it in development? Thanks!

Best wishes, Carla Uranga

benjjneb commented 3 years ago

No it can't. DADA2 makes an assumption that there is a non-trivial fraction of error-free reads in the data, and that just isn't going to be the case with current ONT data. A different algorithmic approach is needed for reads with that high an error rate.

That said, we are watching with interest the continued progress in ONT error rates, and especially the recent talk about "Duplex" sequencing that could achieve the accuracy necessary to work with DADA2: https://nanoporetech.com/about-us/news/oxford-nanopore-tech-update-new-duplex-method-q30-nanopore-single-molecule-reads-0

ps: If anyone at Oxford Nanopore wants to share some Duplex amplicon sequencing data, we'd be interested to take a deep look at it!

skeffington commented 2 years ago

@benjjneb the latest technology available to buy from ONT is yielding Q24. If we're looking at calling ASVs on whole 16S gene amplicons, do you think this is sufficient? Or do we need to wait for the duplex reads and Q30? Thanks! Alastair

benjjneb commented 2 years ago

Will need at least Q30 for DADA2/ASV approach to be appropriate for full length 16S.

skeffington commented 2 years ago

Thanks for getting back to me. Then PacBio it is for now ...

lorenzwidmer commented 1 year ago

@benjjneb Would you still be interested in ONT full length 16S amplicon data? We have a dataset with ~300`000 duplex reads from flower microbiomes with 90 % of bases > Q30 (download link: https://1drv.ms/u/s!Ao-P2TdvTxHxhd80Q6DLsUmZ1edUpg?e=Jx3umc). The data was generated on a MinION Flow Cell R10.4.1 using kit 14 chemistry.

benjjneb commented 1 year ago

Thanks @Lorze !

The semester is winding up, so I'll hopefully have a time to take a peek at this data in the next month or so. Download and format look good.

SwiftSeal commented 1 year ago

Have you had the chance to check this yet? Would be interested to hear how it went - I also have a bunch of Q30+ ONT amplicon data that I might try throwing at dada2 :)

marcomeola commented 1 year ago

Would also highly appreciate some updates on that