Tool request: resources

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1

Hi Jennifer, I was wondering if the KAIJU program is located somewhere on the site, or if its something you can add?

Thanks
Jon

2

Hi Jon,
I googled KAIJU and the top links were for Japanese plant monsters. Do you want the plant monsters or something else? If the latter, an URL to the software might be very handy.
Kind regards,
Igor

3

Hi Igor,

I’m sorry, I had thought that classifier was more well known. Here is the link

https://bioinformatics-centre.github.io/kaiju/

I have used it several times on their web server, which is extremely slow. But it classifies reads that many other classifiers don’t or can’t. It will accept raw reads as input, though it’s possible that QC trimmed inputs may be more accurate.

Thank you,

Jon

4

Hi Jon,
I found this tool in the tool shed
https://toolshed.g2.bx.psu.edu/view/abaizan/kodoja/d4111d1de76f
Are you after this tool or something else?
The repository is not maintained since 2018, and the wrapper might not be compatible with the current Galaxy environment.
Kind regards,
Igor

5

That tool says that it’s strictly for viruses, I sent you the link for the actual KAIJU program. Which identifies bacteria Eukaryotes and viruses.

6

Hi Jon,

thank you for additional info. As the software is not available in the tool shed, someone must write a piece of code called wrapper responsible for integration of the software into Galaxy environment. The wrapper and test data will be deposited into the tool shed. After that the site admins can install the software. I don’t know how long it might take. Ping @jennaj

Kind regards,
Igor

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7

Ok, thank you J

8

Hi @mycojon

As @igor stated, the tool wrapper would need to either be re-written or updated. I’m looking into the details for this one right now, and will get back this week with details.

Warning that it might just be a request ticket unless you are interested in helping with this @mycojon ? If you are, please let me know your Github handle and I can mention you in the ticket/chats. Even just having a scientist who understands the tool, and how they would prefer the form to be organized, plus important options to include, etc is super helpful and opens up the pool of developers that might contribute if the original author is busy or needs support. Most are also community volunteers :slight_smile:

Thanks and I’ve bookmarked this for an update. If you don’t hear back by next Monday, feel free to ping me again.

9

Unfortunately I would not be much help, the programming side is way over my head. As far as I know, its really the only tool that translates sequences into proteins and matches against ncbi refseq and eukaryotes. One nice thing about the program is there is no preprocessing, raw reads are used. Its very sensitive in that it tries to classify all reads. What I like is that it will identify species that are missed using a nucleotide search such as Mycobacterium and Plasmodium (malaria). An example is a shotgun whole blood sample that contained high levels of Mycobacterium Leprae and Plasmodium ovale, completely missed by others.

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6 posts were split to a new topic: Diamond troubleshooting

13

Well, there is not much in the existing Tool Shed entry for the tool wrapper, but I’ve created the request ticket against the IUC. Maybe they can help to triage. Update request for Kodoja database search (version 0.0.8) · Issue #5744 · galaxyproject/tools-iuc · GitHub

For Diamond – search the tool panel with “diamond” and you’ll notice that there is more than one tool wrapper, and one of them is dedicated to creating target databases → Diamond makedb.

But I also see many targets already available in the mapping tool. Use those for the larger public databases like NR and NT.

Help for using any tool →

  1. Scroll to the bottom of a tool form for a short guide, author resources, publications, and a link out to the GTN tutorials it is included in (if any).
  2. For the Diamond suite, the link out points here: Galaxy Training!
  3. General scientific forums and publications are good sources for parameters and methods. Most tools in Galaxy are based on open source tools, and direct usage is usually the same as in Galaxy as far as parameter choices and input/output formats. You’d just be selecting those on the form instead of typing on the command line.
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