search

benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
459 stars 142 forks source link

Dada2 with time series data #1624

Closed Hewang11111 closed 3 months ago

Hewang11111 commented 1 year ago

Hi there, I have a problem about processing time series data using dada2 (groundwater). I took over a project that has been running already for 9 years and has been ongoing. My former colleague ran previous amplicon sequencing (2013 to 2021) with version 1.16 of dada2, but it is understood that the version of dada2 has been upgraded to 1.24. My question is, should I use the latest version to run the new data (from 2021) and incorporate them into the old database or should I continue to use version of 1.16 of dada2 to keep all the data consistency? Many thanks!

benjjneb commented 1 year ago

Staying at 1.16 is fine. Assuming this is short-read sequencing, there have been no substantial changes to the package that would impact the results.

Hewang11111 commented 1 year ago

Thanks a lot! Could you please also let us know if there will be a version with a substantial change from the previous one. So we could update our database totally?

benjjneb commented 1 year ago

Substantial changes will get an announce on my twitter (@bejcal), and release notes on the dada2 website.

The last couple version bumps have been maintenance bumps coinciding with the Bioconductor release tempo, and had little to no functionality changes, so didn't come with announcements.

benjjneb commented 3 months ago

Note: I am not actively maintaining a twitter presence anymore.