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Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)



Hi Andreas and everybody,

I am a regular user of Guppy.  We use it to transform ("basecall") raw
signal output from the sequencers manufactured by Oxford Nanopore
Technologies (ONT) to nucleic acid sequence files in the FASTQ format
accepted by many of the tools that we package in Debian Med.

I think that even if ONT would free Guppy, packaging it would be
a significant challlenge.

 - Guppy is a moving target, and whichever version we would distribute
   in Stable is unlikely to satisfy the users a year later.

 - Upgrades are not drop-in replacements for each other and a laboratory
   typycally needs to install several versions side-to-side.

 - In many cases, a GPU is needed to have Guppy end its computation in
   a reasonable time.  But Debian does not have an infrastructure to
   test GPU computations.

 - As far as I know, Guppy is developed on amd64 and arm64 only.  We
   can therefore expect the usual portability issues.

 - The conversion from raw to FASTQ is done by neural network algorithms
   for which we do not have access to the training data, and therefore
   the freedom to modify Guppy would be limited to the sugar around the
   core algorithms.

In that sense, I think that if we want to distribute a basecaller in
Debian, we should better pick an alternative that is already free.  Some
of them are reported to perform as well as Guppy.  But which one to
pick, and how about long-term mainteance ?

Altogether, I think that we will best serve our users by making sure
that Free basecallers are easy to install on Debian, providing the
standard tools for downstream analysis (we are quite good at this), and
adding value by supporting bioinformatics workflow systems.

Have a nice day,

Charles

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan


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