QIIME 2 2019.10 is now available!

Congratulations to all. If new version is released then do I need to repeat my analysis using new version?

Regards

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Thank you for the updates.

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Congrats guys, and great effort!
Looking forward to novelties.

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@ben,

Its funny because one of the things I love about conda is how many qiime 2 versions i have. I like to work on a single version per project (unless there’s a good reason to switch, like a particular update) and so I keep an enviroment for each project until I’m done and then save that with the analysis scripts. That way, even if its not the most up to date (and it wont be when I publish because there’s always a lag between analysis and publication) I know exactly when I did things. (I actually name my environments differently based on each project.)

So, my advice to @HebaHussein-1981 and @sanda would be to keep whatever environment you’ve been working on for this analysis unless there’s a good reason to update (bug, compatibility, new plugin, critical new feature) and install the latest version so you have the shiny features for your next analysis.

Best,
Justine

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@jwdebelius, Thank you so much for your sincere suggestions. I appreciate that. Now I am enjoying using Qiime2. Kudos to Qiime team @ben.
Many thanks and regards

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Hi all,
Congrats on the new release and thanks for your continuous support to the microbiome people. I have a question in this regard; I was working in a project since last year and for some reason publication was postponed. I updated qiime environment many times (started with V2018. and currently I have qiime2-2109.4. If I installed the new version, should I re-do all the analyses (will I find significant differences in results?) . In general, I used to install new versions but I use it for new running projects.
Thanks
Eman

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thanks for the advice. or this analysis, I use only 6 samples to practice the steps and will run same codes within two days on my whole ~200 samples. So, in this case for my ~200, is it recommended to use the current version as I know the codes or is it better to update so in the publication, I mention it is the latest version? Will be difference in the commands themselves in the update?

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thanks for the advice. for this current analysis as you know, I use only 6 samples to practice the steps and will run same codes within two days on my whole ~200 samples. So, in this case for my ~200, is it recommended to use the current version as I know the codes or is it better to update so in the publication, I mention it is the latest version? Will be difference in the commands themselves in the update?

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@HebaHussein-1981

I would say, if it is not too costly for parallel runs, there’s no issue running them in parallel conda environments. However, unless there was critical plug-in update, there’s not really a hurry to move to the new version. So, I would compete the analysis with the version you’re using (2019.7), and then run and compare results with 2019.10. Ben

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where can I find a robust 16S rRNA end-to-end tutorial for analysing pair-end data, that includes new Qimme2 version?

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Hi all,

I would like to share some experience during analyzed the data through QIIME2. I was attending the NIH QIIME2 workshop in 2018 that was very useful ( I learned a lot ) and I had one issue when I analyzed the data and I asked Evan Bolyen in the workshop , he helped me to solve the issue and be able to run the QIIME2 in my computer. In addition, I asked online help , Nicholas and Mathew were guide me very well to be able run the QIIME2 without any issue. I hope my experience very useful for you and good luck. ~Suad

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Hi @thedam,
As a beginner, I suggest you to go through “Moving pictures tutorial” and “Atacama soil microbiome tutorial”. It helps a lot. All information are very clear, only you need to choose parameters according to your sequencing details. You can also find in Moving pictures tutorial that on what basis and how to choose parameters.
Best wishes

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Hi @HebaHussein-1981,

The change log describes what has changed and the tutorials and help documentation are always a good place to start for whether or not the commands are different! You may still need to pay attention to paths and be careful how you work, but that’s not a QIIME specific issue.

Best,
Justine

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Hi @ben,
While reading the tutorial of the new version, I found a recommendation to use single-end seq since the reads are too short:
“Our samples were amplified using the EMP 515f-806r primers and sequenced on an Illumina MiSeq with a 2x150bp kit. The hypervariable region covered by the primers we used is 290bp long, so with 150bp reads our sequences will be slightly too short to be able to do paired-end analysis downstream. Therefore, we’re going to work with single-end sequences”

Actually, the company that does sequencing for our samples is currently using the same primer set 515f-806r and all of our running projects and future projects will be treated the same. Does that mean it is not recommended to follow the analysis script of paired-end?
Thanks
Eman

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A post was split to a new topic: Functional Databases in QIIME 2

A post was split to a new topic: DADA 2 -9 error code

Hello @Susie which workshop ? can you give me more details please

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Many congratulations to the entire team. great Work. Keep going

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Sorry I missed this, no paired end protocol following the tutorial should be fine. I believe the 515 to 806 region is V4 which is a pretty standard region (although I think some publications say it favors firmicutes).

Ben

Please note, we have a revised release schedule planned for 2020, more preliminary details can be found here:

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