Re: A common test-data package for genome assemblers
On Wed, Jul 13, 2016 at 01:56:39PM -0400, Michael Crusoe wrote:
> This is a great idea!
+1
Please also read the thread
https://lists.debian.org/debian-med/2016/07/msg00090.html
which seems to fit this topic.
Kind regards
Andreas.
> On Wed, Jul 13, 2016 at 11:24 AM, Afif Elghraoui <afif@debian.org> wrote:
>
> > Hi, all,
> >
> > I've had a couple packages that indicate the availability of data
> > outside of the source distribution that can be used to try out the
> > software (and make sure that it actually runs). I didn't think it was a
> > good idea to bundle the data in with the actual package since it doesn't
> > change between releases and would take up too much space on the archive
> > if it was bundled with every upstream tarball.
> >
> > For example, at <http://canu.readthedocs.io/en/stable/quick-start.html>,
> > there are a few reduced datasets that can be used to run assemblies for
> > PacBio and Nanopore sequencing data. Those files can also be used for
> > tests of the sprai package, and possibly also for other long-read genome
> > assemblers. There's also the option of packaging the Assemblathon data
> > for this purpose, or using simulators to generate datasets for testing.
> >
> > Does anyone have suggestions or thoughts on this?
> >
> > regards
> > Afif
> >
> > --
> > Afif Elghraoui | عفيف الغراوي
> > http://afif.ghraoui.name
> >
> >
>
>
> --
> Michael R. Crusoe
> Community Engineer & Co-founder
> Common Workflow Language project
> https://impactstory.org/u/0000-0002-2961-9670
> michael.crusoe@gmail.com
> +32 (0) 2 808 25 58
> +1 480 627 9108
--
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