On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille <[email protected]> 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 -- Jun | He - His - Him
