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gt1 / daccord

d'accord is a non hybrid long read consensus program based on local de Bruijn graph assembly
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is daccordcontig suitable for the error correction with ONT data? #12

Open bitcometz opened 5 years ago

bitcometz commented 5 years ago

Hello, I have used the daccordcontig to do the error correction of scaffolds with PacBio reads, and it works really well, for example, the BUSCO assessment usually achieve above 90%. However, when I used the daccordcontig to do the error correction with ONT(Oxford Nanopore technologies) data, it seems that it did not work well because the BUSCO assessment is about 50%, which was even lower than the Racon. I think it is abnormal. Maybe there is something wrong. Can you give me some advice? Thanks!!!

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gt1 commented 5 years ago

Hi,

I have not run any ONT data through daccord recently. I hope I'll find the time to do so soon.

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bitcometz commented 5 years ago

Thanks! Looking forward to your good news!

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HaploKit commented 3 years ago

Hi, German Tischler.

I also found a similar situation in my cases (Daccord performs much worse(10 times) on ONT reads, compared with PacBio reads, though Daccord performs really well on Pacbio reads error correction.

Have you already tested ONT data on your own? I do want to use Daccord in my applications, but could you please tell me what could be the possible reasons that it performs much worse on ONT data? By the way, may I ask why daccord is not published in a journal since it shows the best performance in terms of accuracy on PacBio data(at least it does in my experiments). Many thanks in advance.