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Hello,
I tried to use ALLHiC and 3D-DNA to scaffold my draft genome. My genome is 9 chromosomes. I used 3D-DNA only get 5 chromosomes. I set 9 groups with ALLHiC. I got 9 Chromosomes (> 25Mb).
Mini…
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Hello @tanghaibao
Tremendous work and more useful than 3d-DNA. I assembled a chromosome-level genome with 20 sequences.
But there is a little problem: where are the unanchored contigs?
The file …
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Hi,
Thanks for developing this useful tool. I am learning how to use it according to the tutorial. However, I have a question about the enzyme sites in the tutorial.
In the step of filtering the…
Tina9 updated
2 years ago
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Dear tangerzhang
Thanks for your tools about assembly of polyploid.
Recently I am doing assembly of a autotetraploid genome, and I follow the workflow #15. After running 3D-DNA, I run the scrip…
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Hi,
When I use ALLHIC to assembly a draft genome, there was an error as follow:
1. tour format to agp ...
Died at /ALLHiC/bin/ALLHiC_build line 12.
I followed this https://github.c…
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Hi, @c-zhou
Is `yahs` do the haplotype-aware scaffolding ? Ex. the downstream of `hifiasm` HiC-phase, we get two haplotype, then cat the assembled fasta together for scaffolding. `3d-dna` did not …
baozg updated
2 years ago
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Hi,
I am attempting to use the ALLHiC pipeline on a diploid highly repetitive plant genome I have assembled.
My Hi-C contains a LOT of PCR duplication, is it recommended to remove these reads before…
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Thanks for the author's contribution.
How can I set stricter parameters if there may be misassembled contigs with default parameters?
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尊敬的开发者：
你好! 在运行简单的二倍体挂载pipline时，发现并行的代码是以染色体数目并行的，可能会造成一定的问题，建议修改为$threads。
```
## ALLHiC_pip.sh 104 l
ParaFly -c cmd.list -CPU $group_count
```
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Hi,
Maybe this is a silly question but I really don't understand how Allhic can connect contigs from the same haplotype.
For example, in a heterozygous diploid genome, there are two regions on …