3d-dna
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aidenlab
3D de novo assembly (3D DNA) pipeline
Hi, my original input has 2,495 contigs but after I used 3d_dna to link them to chromosome levels, there are only 2,484 left. The missing 11 ones were all shorter...
Hi, I am processing a genome with 9 chromosomes, but I only got 8 chromosome-level super scaffolds. How should I adjust the process to get the correct number of chromosomes....
Hi, I've completed a run of 3d-dna using as input a canu raw assembly obtained from 25x WGS mouse data and corresponding Hi-C. I am able to load the `final.hic`...
Hi, I ran 3d-dna with follow command: **run-asm-pipeline.sh IGT-9201.fasta merged_nodups.txt** **The FINAL results seem good, but there was some warnings, what these warnings information means?** :| Warning: no explicit bundle...
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)....
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: >...
Hi, thanks for the wonderful pipeline. When I run the pipeline as following: `run-asm-pipeline.sh -i 5000 -r 0 ../aligned_on_haploid/contigs.fasta ../aligned/merged_nodups.txt` Everything works except the sealing stage. ``` ############### Starting sealing:...
Dear 3D-DNA and JBAT users, This is to let you know that we have put together an extended manual for the genome assembly tools created by the Aiden Lab. The...
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...
Hello! I want to use 3d-dna-master/lift/lift-input-annotations-to-asm-annotations.awk to map my annotation file from input onto the assembly chromosome according to a particular asm and cprops file, but I do not know...
