Extract mitochondrial reads from Oxford nanopore reads

[bioramg]

Hi, I would like to extract plant mitochondrial reads from the whole genome Oxford Nanopore? Do you have any idea which software-related for this? Like GetOrganelle for Illumina reads. Thank you.

[Kinggerm]

I'm working on developing GetOrganelle for long reads. Leave this issue open and I will let you know the updates.

Currently, you can use Flye to assemble a certain amount of original ONT reads, like 2G, which will not be computationally intensive. You can then use get_organelle_from_assembly.py (not get_organelle_from_reads.py) to extract the mitochondrial subgraph from the assembly graph (gfa format file) output by Flye.

The main issue of ONT or Pacbio here is they usually don't generate a good-quality result even with polishing with Illumina, e.g. different IRs in plastome, which I am working on to fix.

[bioramg]

Ok thank you for your suggestion.

[harish0201]

FWIW, I've taken to either blasting/aligning the reads to reference organelle genomes, fetch and subsample those out to generate the assembly.

Depending on the Long-reads type and preparation, I've gotten a single read that represents the genome, so I tend to then trim them off using self alignments or coverage metrics.