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Hi,
I used conda version of 3D-DNA (version 190716) to scaffold my genome.
However, I have not got FINAL files including FINAL.fasta, FINAL.hic although no errors were not observed in log file.
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hello friend
I assembly the genome with juicer and 3d-dna, when run the command "run-asm-pipeline.sh -r 0 raw_scaffold_2.fasta ./aligned/merged_nodups.txt"
its error
![image](https://github.com/a…
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**Describe the bug**
I start to update juicebox from 1.11 to 2.16. The newer version is much faster; it is great. The *.hic + *.assembly generated by 3d-dna can be loaded into juicebox 2.16, but shif…
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With the software, I can successfully reproduce the NA12878 assembly. However, when I tried to use 3d-dna to scaffold my de novo assembly, it failed(I successfully got results with LACHESIS). The spec…
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I have a hap_ctg.fa file with 4.5G, used juicer I got 52.31G merged_nodups_txt,then I used 3D-DNA run-asm-pipeline.sh: 3d-dna/run-asm-pipeline.sh -r 0 hap1234.fa merged_nodups.txt, then, I only got 5…
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Hi,
I'm currently trying to use 3d-dna (version 180922) to assemble a bird genome. The run-asm-pipeline.sh pipeline ran and generate almost all the .hic files except split stage. And, I got the follo…
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Your recent article(Nat. Mat, 2024) proposes a method for predicting DNA origami structure using graph neural networks. I think it's very powerful and exciting. I want to know how to use the function …
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Hi,
I have a 0.9Gbp plant genome with HiFi and Hi-C data. HiFiasm has given me an assembly the correct size with 1000 contigs. Can you please clarify this paragraph in the documentation: https://h…
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We are working on genome assembly of an interspecific hybrid plant having two genomes.
During the 3d-dna step even with haploid mode and diploid, we always had errors saying:
> :( Assembly file …
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Hello,Professor
I have `HiFi + HiC, Nanopore + HiC data`
The draft assembly of `HiFi data` was finished by `Hifiasm`, draft assembly of` Nanopore data` was finished by `Nextdenova` and the resulti…