You are free to use any external scaffolder out there. But I do suggest you try
canu first for nanopore data as MIRA is bound to produce at least unexpected
results when being confronted with nanopore.
B.
On March 7, 2016 at 10:58 AM Adrian Pelin <apelin20@xxxxxxxxx> wrote:
Is it possible to add a scaffolding algorithm based on the data? Essentially
find k-mers in the nanopore read belonging to 2 contigs suggesting they are
linked?
Thanks for the input, Adrian
On Monday, 7 March 2016, Bastien Chevreux <bach@xxxxxxxxxxxx
mailto:bach@xxxxxxxxxxxx ;> wrote:
> > I currently do not plan to support nanopore with MIRA 4 or 5. The
> > fragmentation when feeding ~10% erroneous data does not really surprise
> > me.
B.
> > > On March 7, 2016 at 9:33 AM Adrian Pelin <apelin20@xxxxxxxxx>
> > > wrote:
Hello,
I was wondering if there would be support eventually for nanocorrected
data of nanopore reads. These can now achieve error rates below 10%.
I am trying to feed these as pacbiohq, however am getting very
fragmented assemblies.
Adrian
> >
>