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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Improving the disconnected chromosomes in HiFiasm asm #468

Open Jokendo-collab opened 1 year ago

Jokendo-collab commented 1 year ago

I am running HiFiasm on my data and it seems to be doing well at the HiFi assembly step. When it get to the ONT incorporation we see alot of chromosome disconnection. Is there a specific setting I can apply to improve these assembly? See the attached file withe details

Screen Shot 2023-06-14 at 1 41 28 PM
chhylp123 commented 1 year ago

Could you please show the command line and the log file? I'm just wondering if there is something wrong when running ONT integration.

Jokendo-collab commented 1 year ago

slurm-2094713.out.zip @chhylp123 I used the following command:

hifiasm -o f11_hifiasmconda -t32 -l0 --ul ${ont} ${hifiData} 2> F11hifiasmconda.log

I these some setting I can change to improve the assembly?

chhylp123 commented 1 year ago

Please make sure you are using UL reads in the right way. Please see: https://github.com/chhylp123/hifiasm/issues/453