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Hi
I'm using vg tools v1.50.1 "Monopoli"
I've produced a graph from 7 different genomes of the same species using minigraph-cactus.
I've used the indexes produced from minigraph-cactus with `…
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Hi @AndreaGuarracino,
when I am running the default pggb with DRB1-3123 I do get one graph component aka one community:
![image](https://user-images.githubusercontent.com/10184961/212730802-4634…
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Hi,I got the following error with the command(_**odgi extract -i GRAPH -b BED -o - -c 0 -d 10 --full-range -t 30 -P**_ ), how should I fix it?
Besides, how can I keep more additional inf…
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Hello,
I have been using odgi to visualize several pangenome graphs consisting of a handful of plant genomes, using both the 1d and 2d visualization. One thing that is unclear to me about the 1d vi…
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Hi
I have a question in regards to how VG handles repeat regions.
My genome is around 80% repeats, based on some papers I've read and my results with Repeat Masker.
I'm working with a 20 geno…
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I just started a toil-vg run with `--primary`, but not `--pangenome` or any of the other graph construction options. But I did pass it in a bunch of VCFs, and instructions to filter out NA12878 and th…
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Hi,
Currently comparing a large number of paths in a pangenome graph.
If odgi overlap knows that A overlaps B, will it skip checking if B overlaps A?
I looked at the source code and from what I g…
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As suggested by @heuermh during the BOSC 2021 CoFest - thank you!
- rGFA https://github.com/lh3/gfatools/blob/master/doc/rGFA.md#the-reference-gfa-rgfa-format
- GFA 1.0 http://gfa-spec.github.io/G…
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Hi,
Firstly, I've built a pangenome from 14 genomes. I've used our genome of reference to align the reads and extract the .fasta file from alignment resulting .bam combining these 14 genomes (.fast…
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Hi professors!
I have 19 assembly genome of one species,each assembly genome contains 29 chromosomes.I want to construct a graph from the 19 genomes using PGGB. I firstly combine the 19 genome into a…