Racon compatibility?

[cnk113]

Hello,

I was wondering if you planned on implementing racon within the tool? Or maybe an output that racon can take?

Thanks,
Chang

[yangao07]

Hi,
Thanks for your interest in TideHunter!
I think very likely that Racon will improve the quality of the consensus produced by TideHunter.

[yangao07]

I don't have any plan recently since I have been occupied with some other projects.
Do you have any suggestions about that?
Thanks!

[cnk113]

Sorry I got sidetracked, but I was planning on using MarginPolish + HELEN to improve the accuracy.
I was thinking of using the first consensus of the POA (as it is currently), and then use the subreads by realigning to the consensus and pass that into MarginPolish.
Does that make sense?

[cnk113]

So I guess would it be possible for Tidehunter to output all the subreads as well?

[yangao07]

I see your point and I think it makes sense.

[yangao07]

I will try to add additional output for the subreads information so that you can implement your idea.
Will update a release when it is done.

[yangao07]

In the latest release (https://github.com/yangao07/TideHunter/releases), the subread position information is now output as a ',' separated string in the output file.
Please try it and let me know if it works for you!
Yan

[cnk113]

Thanks, I'll try this over the weekend.

[yangao07]

Just found a bug in v1.2.0, please not try it until I fixed it.
Sorry about that.
Will get back to you later.

[yangao07]

Please try the latest version, v1.2.1 (https://github.com/yangao07/TideHunter/releases).
Bugs are fixed now.

[yangao07]

Check out the -u/--unit-seq option in the latest release: v1.4.0.
It will give you all the unit sequences of each tandem repeat.