-
Hi!
First, what's the difference between "3D model reconstruction by 3DMax" and "3D model reconstruction by LorDG"? How to choose?
Second, if I want to build 3D chromosomes and genome models use …
-
Hello ! I hope for some solutions for my questions. My Bash version is: GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu), and my 3d-dna version is version 180114. When running run-asm-pip…
-
Hello,
I want to run the diploid portion of the pipeline to identify/remove alternative haplotypes if i want a haploid representation of the hybrid genome,should I run the `awk -f ${path_to_3ddna}/ut…
-
I would like to start generating some real examples of packages
if @Ilia-Kosenkov and @clauswilke could help.
We could, for example:
* Show memory mapped files with parallel parsing (such as JS…
-
Hi Dr.Wang
Thank you for your excellent work. We encountered an issue when running the example workflow. Could you provide some advice? Additionally, could you supply some information and code on h…
-
Hi,
Recently, I have used Juicer to analysis my data. I got some results in the aligned file, as follows, but it did not generate merged_nodups.txt. I do not know how to solve it. Can you help me? T…
-
Hi,
I'm trying to assemble a homozygous plant genome (diploid) with Hifiasm using HiFi and Omni-C data with the following Command line :
hifiasm -t 40 -o Hifiasm_output --h1 Omni-C_R1.fastq.gz --h…
-
Hi,
I have pacbio Hifi read assembly using Hifiasm. Hifiasm gave me much less fragmented assembly as compared to other tools. However, there are more contigs. Some of the them are quite small and…
-
I tried running `alt_frac` and `coverage` scoring methods on the same inputs. Then I calculated the VAF based on alt and ref reads from the `coverage` output matrices. Most of the values agree, but so…
-
Hi,
I have a haplotype resolved assembly done with hifiasm (HI-C) and Hifi data for a plant genome. I would like to use the 3d-DNA pipeline for the scaffolding and produce a haplotype-resolved fina…