Hi Adrian,
haven't worked with Nanopore data myself yet, but maybe I can give you a
lead and you haven't stumbled across the following tools.
At the moment the best choice for Nanopore data seems to be Canu
(https://github.com/marbl/canu, further development of the Celera
Assembler) following up with Nanopolish
(https://github.com/jts/nanopolish). SPAdes supports Nanopore as well
but Canu seems to be superior.
Mira with its greedy and OLC algorithms might actually be a good option
for Nanopore reads. Would be interesting to compare assemblies.
Hope this is useful information.
Cheers,
Andreas
--
Andreas Leimbach
Universität Münster
Institut für Hygiene
Mendelstr. 7
D-48149 Münster
Germany
Tel.: +49 (0)551 39 33843
E-Mail: aleimba@xxxxxxx
On 07.03.2016 15:33, Adrian Pelin 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
