Mitochondrial genome assembly

[fergsc]

Hi,

Would trycycler be suitable to use on mitochondrial genomes?

The general plan would be:

1. Bait reads from a closely related mitochondrial genome/s.
2. Subsample ~6 times.
3. Assemble with Flye and miniasm.
4. Run Trycycler on the 6 assemblies

thanks.

[rrwick]

Yes, Trycycler should be suitable for mito genomes, and you can also give Autocycler a try - it's usually easier and faster than Trycycler.

For both Trycycler and Autocycler, the main requirement is that your input assemblies are mostly complete, i.e. you can get your entire mito genome assembled into a single contig.