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Hello,
I ran the test data in the login node of HPC cluster:
```
nextflow run /public/home/zyqi/pan-TE-analysis/GraffiTE/GraffiTE/main.nf \
--assemblies assemblies.csv \
--TE_library huma…
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Hello,
I'm having an issue while loading my .gfa file of a pangenome I created using the mingraph-cactus pipeline.
For context it's a pangenome created from 1 reference + 2 genomes with the follo…
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Hi,
I am trying to use PanGenie to genotype personalized minigraph-cactus graphs generated by `vg haplotypes`. In the [personalized pangenome paper](https://www.biorxiv.org/content/10.1101/2023.12.…
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Dear sir, I constracted a graph pangenome by vg aotuindex( line + vcf). I want to extact a loci gene, But I encounter an error.
```
$ odgi extract -i merge.combined.giraffe.og -o path111.og -b p…
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### Submitter Name
Martin Maiers
### Submitter Affiliation
National Marrow Donor Program
### Submitter Github Handle
mmaiers_nmdp
### Additional Submitter Details
_No response_
### Which event…
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As mentioned in #149 I get a segmentation fault on branch `walks`, which I don't get on branch `dev` with my Macbook Pro. Example GFA file I obtained from the Minigraph-Cactus pipeline can be found he…
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Dear developers,
My issue is very similar to https://github.com/ComparativeGenomicsToolkit/cactus/issues/1212. I decided to open a new one, considering I work with the latest release of Minigraph-C…
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We tried out manubot for [our manuscript](https://github.com/jmonlong/manu-vgsv) and one part that required some manual work was dealing with the supplementary information. Maybe we missed something a…
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Hi,
I would like to use Truvari to merge SVs deconstructed from a pangenome graph. The VCF usually has many records with a lot of similar alleles (e.g., only 1 bp difference). An example from HPRC …
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Thanks for your development of this useful tool!
I have a question about pantranscriptome.
I have several assembled and annotated genomes. In pangenome analysis, the annotated gene could be cluste…