Long reads - nanopore
Psy-Fer opened this issue · comments
Hello,
I'm interested in using this tool, but before I go down the rabbit hole of installing this tool, I would like to know if it works with long read tech, such as nanopore? for example, skipping to the diri_sampler step?
Cheers,
James F.
Hello James,
Regarding your request for using nanopore long reads:
- Yes, it is a request that we are currently also getting from other users and we would definitely consider it. Do you have example data that you could provide us?
Regarding diri_sampler :
- This step is the actual Dirichlet distribution. It's the statistic method on which ShoRAH relies. If you skip it, shorah has no results. It needs to be run. But currently there is a hard-coded sample size inside, making it impossible to use long read, and this needs to be adapted. The mathematical method itself should be working on longer reads too.
We're currently busy with the upcoming BASELLIFE / [BC]2 conference. I'll be available to try helping you around this in two weeks.
Hey,
Thanks for the reply.
I think my meaning was lost in my language.
"skipping to", as in, start the process at the Dirichlet distribution step.
We are looking at some long read virus data.
Oh, and have fun at the conference.
Let me know if there is any progress or way I can help.
We are looking at some long read virus data.
Out of curiosity, do you have a bit more information about your experiment ?
Let me know if there is any progress or way I can help.
Some sample data would be nice, even more so if you happen to know what you would expect from the data.
Hi, is there any update on the use of Nanopore reads with this tool?
Thanks,
Ed