Help: Seeking source code of guppy base caller (Was: Idea wanted: What is the most key open source projects to fight COVID-19?)

[Andreas Tille <tille@debian.org>]

Hi,

I also tried my luck to find the source code for guppy base caller - but
failed.  It would of great help if somebody could find out.

Thanks a lot Jun for giving detailed hints so far

     Andreas.

On Fri, Apr 24, 2020 at 08:41:22PM +0200, Jun Aruga wrote:
> > > https://github.com/nf-core/nanoseq/blob/master/bin/scrape_software_versions.py
> > > guppy
> > Missing in Debian.  Is it this project
> >    https://staff.aist.go.jp/yutaka.ueno/guppy/  ?
> 
> Hi, Andreas,
> No, it seems that guppy is a base caller provided by Oxford Nanopore
> technologies.
> 
> ```
> $ pwd
> /home/jaruga/git/nf-core/nanoseq
> 
> $ grep -r guppy *
> ...
> conf/base.config:      container = 'genomicpariscentre/guppy-gpu:3.4.4'
> conf/base.config:      container = 'genomicpariscentre/guppy:3.4.4'
> ...
> 
> Then check the containers Dockerfile.
> 
> https://hub.docker.com/r/genomicpariscentre/guppy/dockerfile
> > wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_${PACKAGE_VERSION}-1~xenial_amd64.deb
> 
> https://hub.docker.com/r/genomicpariscentre/guppy-gpu/dockerfile
> > wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_${PACKAGE_VERSION}-1~xenial_amd64.deb
> ```
> 
> It might not be open source software, seeing the following page.
> Here is a user's page about guppy in Japanese. I could not find the
> English page.
> You can see the guppy's screen shot on
> https://community.nanoporetech.com/downloads page.
> 
> http://kazumaxneo.hatenablog.com/entry/2020/01/19/145940
> 
> > Thanks again Jun for your very helpful contribution
> 
> You are welcome. Let me comment on your comments later.
> 
> Cheers,
> Jun
> 
> -- 
> Jun | He - His - Him
> 
> 

-- 
http://fam-tille.de