Forum:New Aligner Tool - Would you be interested in this ?

Question

[Andrew_MacGregor]

Instead of trying to build a "silver bullet" aligner that efficiently runs on 50bp to 50kbp reads, I'm trying to build a tool that would automatically select the best out of 4 or 5 different aligners for you to use, given your input data type and hardware platform.

I've been working on a project to evaluate the performance of many different aligners on different platforms, and I think this would be a neat way to use the data.

Below is a demo GUI (of course, a CLI would come before the GUI).

Is this something you would be interested in using?

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PS - thanks for the great responses you sent me earlier this week about what aligners you use!

[GenoMax]

Are you going to provide instructions for people to install those 4-5 programs using conda etc. Otherwise this GUI will be of no use to a layperson.

It is commendable that you appear to be trying to set right expectations for run times but are you taking into account the size of input data/hardware/memory available or are those more of a general estimate?

[Corentin]

This is an interesting idea, However, there is a tool doing something similar: http://teaser.cibiv.univie.ac.at/, have you checked it ?

[Andrew_MacGregor]

That looks great! I definitely like its paper. I'll see how well it does this weekend.

[Andrew_MacGregor]

I'm definitely impressed by Teaser. Until I find some shortcomings with it, I'll hold off on developing my tool.

Answer 1

[Devon Ryan]

While I might not personally use such a program (I basically am that program), I think it'd be quite useful for people new to the field so they don't need to post the umpteenth "which aligner should I use?" question. So go for it! Anything that makes getting people quickly started with an analysis is a good thing in my book.

Answer 2

[Joe]

Sounds like a great idea (particularly if it has a GUI for beginners who are all to often presented with reads and have no idea where to go next!).

I've often considered doing a similar (but much lighter) thing to make my own life easier. Basically a bash wrapper around different aligners with some heuristics to figure out parameters etc. I can definitely see a use case!