I have a bunch of sequences output from Dada2 that apparently had been previously assigned with uclust and qiime1. I wanted to see what Qiime2 did with these sequences but did not want to load up my laptop with this stuff as I am short on resources. I downloaded the master.zip from github but just observed it contains a lot of python without much else besides the core modules( no fasta files or references etc ) . Are there any public results that were run to validate/benchmark qiime2 assignnments before release? I would like to test my code against any data like that. Thanks.
And, yes I would note that the use of “artifact” in almost all field relates to an error in the processing not added information
Is qiime2 available as a service for testing before loading onto my computer?
Yes, you can use the AWS deployment option, but there will most likely be fees incurred with Amazon Web Services.
QIIME 2 is a framework that adds functionality via plugins - typically plugins are just some existing tool in the microbiome bioinformatics space (e.g. deblur, dada2, mafft, fasttree, vsearch, cutadapt, etc). QIIME 2 is not a set of scripts, so you will need to use one of our official installation methods to install it.
Please see my note above - QIIME 2 is the glue for wiring together existing tools. If you have a question about one of those tools' validation, check their respective paper/docs/forum/etc.
In QIIME 2 the term "artifact" is like an "archeological" artifact - it is a treasure, or a valuable resource produced by some past process or processes (like running a command). Think of Indiana Jones.
Thanks. I guess then if I built my test code as a plugin in theory it would
make side by side tests easier. How would you characterisze qiime2 for c++ tool development? I saw a post here earlier on plugin writing but can’t find it now.
In any case, I gather that this is mostly to help workflow in production setting and not som much a tool R and D platform. Also I got the impression that things like uclust worked with qiime1 and for whatever reason did not apply here.
Normally an artifact is something you stumble into or maybe find by searching rather than create with purpose. I don’t argue about words and often abuse them mysefl but this did seem a bit striking lol. Image processing artifacts may be artistic but you find them either by seeking them out as theoretical concerns or stumbling onto them from a user report lol.
I'm not quite sure what this means - QIIME 2 is not an IDE.
As I mentioned above, QIIME 2's role is to orchestrate coordination between pre-existing tools.
If you have any additional questions can you please ensure that your questions are clearly identifiable, and, appropriate to the given topic they are posted under. Feel free to make additional topics to make sure this is maintained. Thanks!
