Looking for software to generate reports from raw data

5 weeks ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Galaxy can process the data and keep track of that information in a reproducible way that can be shared with others, but that is technical information. Many tools generate analysis reports but those can also be a bit technical, especially for doctor/patients. Anyone actually running the analysis would find both very informative/useful.

The information available could be parsed out into a report of your own design to format/simplify the analysis results.

If you want to try out Galaxy and see if what it provides is enough, linked below is how to use it. Use public or tutorial data and avoid using your real patient data on any public Galaxy server. You'll need to set up a Galaxy server behind a proper firewall to use it with clinical patient data.

Ecosystem: https://galaxyproject.github.io/
Resources: https://galaxyproject.org/use/
Tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD COMMENT • link written 5 weeks ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer, thank you so much for your reply. I am not sure if I was clear on what I need to be done. So we will be using the NextSeq 500, which will spit out the raw data. What I am loking for is software that will interpret the data, as well as put it into a clinical report format, is that something that Galaxy can do? or maybe you can suggest another software that does that? Thank you, Eugene

ADD REPLY • link written 5 weeks ago by evreychik1 • 0

Galaxy can certainly analyze the data but you would need to take those conclusions and put them into a report format that meets your needs. What to include sounds highly customized from what you've explained.

That said, you could write your own Galaxy tool that takes in results, reformats, and include that in your workflow.

For an example of a summary report generating tool, see "MultiQC". For a simple example, run FastQC on some set of fastq data (at least two distinct datasets) then use MultiQC to combine the results into a summary report. If you like how that tool combines results, you could extend it to read the results from other tools, add in more customized options (special headers or labels), and the like.

For an example of a Clinical-use version of Galaxy, please see this publication: An architecture for genomics analysis in a clinical setting using Galaxy and Docker Digan et al https://doi.org/10.1093/gigascience/gix099. Related tweet:

An Architecture for Genomics Analysis in a Clinical Setting Using Galaxy and Docker @willdigan et al. https://t.co/NesNGTfEqh #usegalaxy pic.twitter.com/qIGA4F68CP
— Galaxy Project (@galaxyproject) October 20, 2017

If you do find some other line-command tool that does what you want, it could also be wrapped for Galaxy. Nearly any tool can be wrapped. People use Galaxy for all sorts of analysis, not just genomics.

If you choose to do development, be sure to use Planemo. It will make the process much easier. https://planemo.readthedocs.io/

ADD REPLY • link modified 5 weeks ago • written 5 weeks ago by Jennifer Hillman Jackson ♦ 25k

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