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Nanopore specific assembly tool of Mitochondria

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!

assembly nanopore mitochondria
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updated by colindaven colindaven • written by adarsh • adarsh

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?

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written by adarsh • adarsh

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)

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written by lieven.sterck lieven.sterck

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)?

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written by colindaven colindaven

1 answer

Options for nanopore assembly

  • flye
  • shasta
  • hifiasm with the new --ont mode
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written by colindaven colindaven

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