Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <tille@debian.org> wrote:
>
> Hi again,
>
> this brings up again my point: We *really*, *really* should take the
> chance right now to ask upstreams for free licensing. The time is good.
> We just need somebody who is really doing this.
For us, the free licensing is good. But for the company nanopore
technologies it is their core competency.
I am not sure we can make it happen, but it might be worth trying to ask.
> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote:
> > Extracting the linked deb, one finds a binary and a very restrictive
> > license. I do not believe that guppy source code is available nor it is
> > likely to become available any time soon.
> >
> > While some of their other basecallers have source code available, I would
> > not call the license OSS:
> > https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt
I found guppy client software that might be an alternative to use
guppy's function.
https://github.com/nanoporetech/pyguppyclient
As Michael mentioned, checking other basecallers for nanopore, then
communicating the nf-core/nanoseq project using the alternative base
caller optionally.
I found an interesting document about the basecallers.
https://github.com/rrwick/Basecalling-comparison
Performance of neural network basecalling tools for Oxford Nanopore sequencing
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y
> In this study, we tested four basecalling programs developed by ONT – Albacore, Guppy, Scrappie and Flappie
> ...
> We also tested Chiron (https://github.com/haotianteng/Chiron), a third-party basecaller still under development that uses a deeper neural network than ONT’s basecallers [3].
The third party basecaller Chiron's license is Mozilla Public License, v. 2.0.
https://github.com/haotianteng/Chiron/blob/master/LICENSE.md
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