Daniel Vaulot

Dear Juan This is an interesting case which shows that V9 in some case is not really a good marker. I aligned the sequences that matched at 100% your Tara...

Hi Soluna Do you exactly where the program gets stuck ? Are you using dada2 under R ? Cheers. Daniel

Hi Soluna and Peter I have been using dada2 version 1.8.0 in R and did not have this problem (16 Gb of memory). I just saw that there is a...

Hi Soluna In the end, I decided not to release a V4 or V9 version of PR2. I used quite universal primers to cut the pr2 sequence to V4 and...

Dear Juan Thanks a lot for the feedback. I will try to update for the next release of PR2. Best. Daniel

Just as a comment, now PhytoRef (plastid sequences) are integrated into PR2 version 5.0.0. Also some errors have been corrected. So I think it is better to retire PhytoRef.

In the next version of PR2, there will be a link to EukRibo which has annotation for the V9 region. So it will be possible to select only sequences that...

The dino sequence will be labelled as chimera in version 5.0.0 soon to be released.

Hi Krzysztof Answers to your two excellent comments: In GenBank some sequences may be labelled Genus_sp. although they correspond to a specific species, but the person who deposited the sequence...

Hi Thank you for your feedback. PR2 taxonomy is a fixed rank taxonomy. The current # number of levels is 9 (see https://pr2-database.org/documentation/pr2-taxonomy-9-levels). We had to make choices that mean...