Unable to converge

[simleopold]

Hi,

I'm a student working on a project to estimate the size of a species' genome. I generated a histo file from ONT Minion datas and genome scope was unable to converge. Does the problem come from the long reads ?

Thanks for your help.

[mschatz]

Yes, ONT reads have a higher error rate that obscures the kmer profile. I would suggest trying to run an assembly and then aligning the reads to the assembled contigs so that you can estimate the average coverage. Then if you sum up the lengths of all of your ONT reads and divide by the estimated coverage you will get a very rough idea of the expected genome size. It will be very rough but should get you an order of magnitude estimate, e.g. if you have 100GB of reads, and your average coverage is 40x, you can estimate the genome is 2.5GB. Hope this helps Mike

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On Mon, Feb 5, 2024 at 3:48 AM simleopold ***@***.***> wrote: Hi, I'm a student working on a project to estimate the size of a species' genome. I generated a histo file from ONT Minion datas and genome scope was unable to converge. Does the problem come from the long reads ? Thanks for your help. — Reply to this email directly, view it on GitHub <#120>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABP34YRY5UGAU22X436QLTYSCMGBAVCNFSM6AAAAABCZXH4LCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYTOOJYGM3DKNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[simleopold]

Thank you for your help, do you know any tool capable of doing this ?

[mschatz]

I dont know of a push button solution. I would start with minimap2 to align the reads to your contigs, and then bedtools or samtools to compute the read coverage. From this I would plot a histogram of the reported coverage (using R/python) to visually inspect what looks to be the average coverage. Good luck! Mike

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On Tue, Feb 6, 2024 at 9:06 AM simleopold ***@***.***> wrote: Thank you for your help, do you know any tool capable of doing this ? — Reply to this email directly, view it on GitHub <#120 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABP344O6GW53LLK72RPLIDYSI2FPAVCNFSM6AAAAABCZXH4LCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRZG42DOOJRGU> . You are receiving this because you commented.Message ID: ***@***.***>