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@golu099 brought up [GAPPadder](https://github.com/simoncchu/GAPPadder) as a tool to potentially replace [Gap2Seq](https://github.com/rikuu/Gap2Seq) for filling gaps in seq coverage between scaffolded…
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I'm working on scaffolding a HiCanu assembly for a shark species that has had duplicates purged. It was assembled with ~45x PacBio Hifi (Median length: 13,710 bp; Mean length: 13,590 bp; Max. length: …
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Hi Nadolina!
Thanks for setting up the steps for dual curation. I am wondering if I should scaffold the haplotipic assemblies with YAHS separately before concatenating and dual curating them on Prete…
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Hi Kris,
I have predicted viral scaffolds from 54 samples assemblies. I tried to use:
vRhyme -i fasta -r paired_reads_folder/*.fastq -t threads -o output_folder --method longest
But it shows an e…
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Hi there,
I have ran the run_yahs.sh file with the test assemblies provided and generated a .hic and .assembly file. After putting both files in JBAT, I noticed that you can only manually edit the…
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Hello sir,
Long time fan and user of Flye, Abruijn, etc.
I have three datasets:
- PacBio HiFi
- 90-95% accurate ultra-long ONT
- Hi-C
I know there are other assemblers that may out-perform…
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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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New GO arrangement
iron-sulfur cluster assembly complex (GO:1990229)
|_cytosolic [4Fe-4S] assembly scaffold complex (GO:1904564)
|_cytosolic [4Fe-4S] assembly targeting complex (GO:0097361)
…
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I have assembled multiple versions of contig genomes, and I would like to use the gala software. Do these genomes require chromosome scaffolding before I input them into the gala software?
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Hello,
I would like to ask what do you usually do when encountering this type of patterns in the scaffolds:
![image](https://github.com/user-attachments/assets/c66139df-15e4-4083-8799-7a67334cdb…