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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Using Nanophore reads for Mitochondrial Genome assembly #215

Closed Millawati closed 8 months ago

Millawati commented 8 months ago

Hi, can we use Nanophore reads for the Mitochondrial genome assembly using Novoplasty? Or it still only for Illumina data?

ndierckx commented 8 months ago

Only for Illumina data, do you want to combine short and long or only long? Will soon have a targeted long read assembler available: https://github.com/ndierckx/NOVOLoci

Millawati commented 8 months ago

Hi,

Thank you for your respond. We want combine both short and long. Is there any assembler you can you suggest?

On Fri, 24 Nov 2023 at 9:31 AM, Nicolas Dierckxsens < @.***> wrote:

Only for Illumina data, do you want to combine short and long or only long? Will soon have a targeted long read assembler available: https://github.com/ndierckx/NOVOLoci

— Reply to this email directly, view it on GitHub https://github.com/ndierckx/NOVOPlasty/issues/215#issuecomment-1825046216, or unsubscribe https://github.com/notifications/unsubscribe-auth/BEGIWN2LSS3PHBPC5P3QOI3YF72IDAVCNFSM6AAAAAA7XJDYNKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRVGA2DMMRRGY . You are receiving this because you authored the thread.Message ID: @.***>

ndierckx commented 8 months ago

Don't think there are many, can't think of any at the moment, ask google :)

I will include long reads to NOVOPlasty in the future, but don't have the time the next few months to finish it. I have an unpublished version that is not ready to make public, I just helped someone for one assembly: https://www.mdpi.com/1422-0067/24/4/3976

But doesn't the assembly work with only short reads, or is it a plant mitochondrial genome?

Millawati commented 8 months ago

Alright. Thank you for your help. Really appreciate it.

On Fri, 24 Nov 2023 at 10:19 PM, Nicolas Dierckxsens < @.***> wrote:

Don't think there are many, can't think of any at the moment, ask google :)

I will include long reads to NOVOPlasty in the future, but don't have the time the next few months to finish it. I have an unpublished version that is not ready to make public, I just helped someone for one assembly: https://www.mdpi.com/1422-0067/24/4/3976

But doesn't the assembly work with only short reads, or is it a plant mitochondrial genome?

— Reply to this email directly, view it on GitHub https://github.com/ndierckx/NOVOPlasty/issues/215#issuecomment-1825740672, or unsubscribe https://github.com/notifications/unsubscribe-auth/BEGIWN7OY7U337JE6SKBO73YGCUGRAVCNFSM6AAAAAA7XJDYNKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRVG42DANRXGI . You are receiving this because you authored the thread.Message ID: @.***>