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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
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ONT Duplex Reads #413

Open WenyuLiang opened 1 year ago

WenyuLiang commented 1 year ago

Thanks for the wonderful tool! Given the great improvement made to ONT duplex reads, I'm wondering if hifiasm can also be adapted to assemble duplex reads by changing some parameters? If it can, what parameters you would suggest me to try?

chhylp123 commented 1 year ago

I am also interested in the results. In theory, duplex reads should work default parameters.

WenyuLiang commented 1 year ago

Thanks for your response. I will have a try.

OZTaekOppa commented 1 year ago

Hi @WenyuLiang and @chhylp123,

Hope this email finds you well.

I am really interested in your duplex approach for humans, plants and animals. Is there any progress? Adding to this, is there any chance to use the Pore-C approach over Hi-C reads?

FYI, https://github.com/epi2me-labs/pore-c-py https://github.com/nanoporetech/Pore-C-Snakemake

Based on the manual, it says as below:

Single-sample telomere-to-telomere assembly with HiFi, ultralong and Hi-C reads

hifiasm -o HG002.asm --h1 read1.fq.gz --h2 read2.fq.gz --ul ul.fq.gz HG002-HiFi.fq.gz

HG002-HiFi.fq.gz: Can be replaced with ONT duplex reads --h1 read1.fq.gz --h2 read2.fq.gz: Is it possible to use Pore-C data instead of Hi-C reads?

If not able to integrate with the current pipeline, what would be the best way to produce phased T2T assembly using PBHiFi (can be replaced with ONT duplex), ONT Ultra-Long and Pore-C data?

Looking forward to your reply!

chhylp123 commented 1 year ago

We do happy to have a try. Could you please point us where can we find good Pore-C data?

OZTaekOppa commented 1 year ago

Please see the below info.

Pore-C tools: https://github.com/nanoporetech/pore-c/blob/master/README.md You can find the Sample data here.

Alternatively, you could access the data from this link https://www.ncbi.nlm.nih.gov/search/all/?term=PRJNA941083. This is the one that I worked with colleagues.

While I tested only the snakemake version of the Pore-C pipeline but the latest version is nextflow (pore-c-py) in https://github.com/epi2me-labs/pore-c-py. If possible, it would be better to try the latest version.

It would be wonderful if hifiasm can accept the duplex reads and Pore-C data from ONT.

If there is any issue, please let me know.

Cheers!