Can I use MITObim with Nanopore reads?

[hungweichen0327]

Dear community,

According to the manual of MITObim, this useful software can use PacBio long reads for mitochondria assembly. Can I use Nanopore long reads, too? Thank you.

[L1curry]

nobody？

[chrishah]

Hi,
MITObim and the version of the assembler (MIRA) it currently supports was developed before Nanopore came up and it hasn't yet been tested with this kind of data, at least not by me, I am afraid. Worth trying with the --platform pacbio setting, though.
cheers,
Christoph