Any advice for improve the scaffolding level using endhic ?
zhenwenliu opened this issue · 1 comments
zhenwenliu commented
"Thank you for your excellent work on genome scaffolding. I would like to seek your help to further improve the scaffolding for our genome.
We are studying a diploid plant species with an expected chromosome number of n=10. First, I used hifiasm with Hi-C data to assemble two haplotype-phased contig genomes, then scaffolded them using a combination of Chromap, YAHS and Juicer. The N50 of my contigs was about 6.3 Mb, not high. Then, I used the scaffolded Hap1 and Hap2 assemblies as input to HiC-Pro, with 1 round of endhic scaffolding. For Hap1, I obtained 9 chromosomes. For Hap2, I obtained 5 chromosomes. The contact maps in Juicebox show this result.
I have several questions:
- Are there any issues with my current scaffolding workflow?
- What can I do to directly obtain 10 chromosomes for each haplotype using endhic? adjusting parameters or using another pipeline?
- I find Juicebox not very user-friendly. The chromosome boundaries seem unclear to me. Also, Juicebox only shows chromosome blocks, without scaffolds or contigs. Why is that? Is it possible to manually adjust the present contacts?
- Any other suggestions to improve my scaffolding are most welcome.
I would greatly appreciate your expert advice on optimizing the genome scaffolding. Thank you again for your kind assistance."
fanagislab commented
If your genome is diploid, just use hap1 or hap2, one set of contigs, as the input of scaffolding. You can also try the p_ctg by adding "--primary" parameter to hifiasm. Considering your contig N50 is relatively lower, EndHiC may not be suitable. Please try to use Yahs.
***@***.***
From: zhenwenliu
Date: 2023-08-16 07:51
To: fanagislab/EndHiC
CC: Subscribed
Subject: [fanagislab/EndHiC] Any advice for improve the scaffolding level using endhic ? (Issue #6)
"Thank you for your excellent work on genome scaffolding. I would like to seek your help to further improve the scaffolding for our genome.
We are studying a diploid plant species with an expected chromosome number of n=10. First, I used hifiasm with Hi-C data to assemble two haplotype-phased contig genomes, then scaffolded them using a combination of Chromap, YAHS and Juicer. The N50 of my contigs was about 6.3 Mb, not high. Then, I used the scaffolded Hap1 and Hap2 assemblies as input to HiC-Pro, with 1 round of endhic scaffolding. For Hap1, I obtained 9 chromosomes. For Hap2, I obtained 5 chromosomes. The contact maps in Juicebox show this result.
I have several questions:
Are there any issues with my current scaffolding workflow?
What can I do to directly obtain 10 chromosomes for each haplotype using endhic? adjusting parameters or using another pipeline?
I find Juicebox not very user-friendly. The chromosome boundaries seem unclear to me. Also, Juicebox only shows chromosome blocks, without scaffolds or contigs. Why is that? Is it possible to manually adjust the present contacts?
Any other suggestions to improve my scaffolding are most welcome.
I would greatly appreciate your expert advice on optimizing the genome scaffolding. Thank you again for your kind assistance."
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