Nanopore specific assembly tool of Mitochondria

Question

[adarsh_munna]

Hi,

I have nanopore ultra-long sequenced data of mitochondria of a plant species. I need to perform assembly for which I am unable to find a nanopore specific tool. Other than general assemblers like Flye, are there any specific tool that can be used.

Thank you!

[lieven.sterck]

why do you assume that Flye would not work here?

I don't have any in mind immediately but perhaps look for a plasmid assembler with ONT data input?

A quick google search resulted in for instance this:

PlasCAT: Plasmid Cloud Assembly Tool

WeFaceNano

[adarsh_munna]

I have already tried Flye Assembly and it gave 880 contigs. It is not able to assemble the genome properly. Can we use a plasmid assembler for mitochondria? Is it because of the circular structure?

[lieven.sterck]

How much data do yo have as input for this assembly? If the coverage is too high you light consider to down-sample it a bit, that might improve continuity of the assembly.

Yes, the circular structure might hinder the analysis (though I thought that flye could handle that)

[colindaven]

How many of those 880 contigs were mitochondrial (try to annotate the genes) and how many looked like contamination (wrong species, non-mitochondrial genes etc). What is your N50 - both of your reads and of the assembly. How big do you estimate the mitochondrion will be (check related species)?

Answer 1

[colindaven]

Options for nanopore assembly

• flye
• shasta
• hifiasm with the new --ont mode