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I have assembled for a genome a "suspected" highly hetrozygous genome using hifi.
The assembled genome size is 8.2G, which gives following BUSCO results.
Could you please help me understand how t…
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Hello,
I am trying to run hisatgenotype. I installed both hisat2/2.2.1 and hisatgenotype. Here's my exact command:
```
python3 /cluster/home/user/hisatgenotype/hisatgenotype --base hla --locus-li…
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The document says that the graph generated by Minigraph has no cyclic, which from my understanding, is a directed acyclic graph. However, when I checked the file `hprc-v1.0-minigraph-grch38.gfa`, I fi…
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This is a thread to discuss how to build genome graphs with haplotypes that preserve the privacy of the genomes that the graphs were built from.
As a test data set, I downloaded a piece of chr20 fo…
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Thank you very much for providing such a useful tool!
I successfully used it to assemble the genome of a diploid orchid. I want to get the gfa file of the diploid assembly, similar to the hifiasm_r…
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Hi,
I only have two genome and I want to build a graph via cacuts. But a tree is needed for cactus. How can I construct tree based on two genome (maybe I cann't build tree contained two genome)?
…
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Hi,
My name is Maggs. We recently generated a pangenome graph. We used soft-masked genomes as input. Since then, we revised the masking. The regions that are soft masked differ rather substantiall…
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Hi,
I need to run TE-Aid in parallel but it causes errors because of using shared resources.
I tried this command (to copy TE-Aid to a temp file for each process so it doesn't use the same databa…
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Hi, I want to construct a whole-genome variation graph with vgtools. The reference genome I have contains more than 3,200 scaffolds, and I don't want to abandon them while constructing the graph.
I…
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Hello
Thank you for this great tool.
I am trying to call TE insertions on a tree genome which is ~ 830 Mb.
My config.yaml file is as follows:
```
# all path can be relatif or absolute
D…