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Hello,
I used the HPRC pangenome (https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph/hprc-v1.0-minigraph-grch38.gfa.gz) to do the analysis. My processes to …
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Hi
I have a whole chromosome graph from a pangenome alignment which includes paths along different genomes (20). I've embedded genes/exon/CDS into the graph based on a single path (the known and we…
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I'm having some trouble with `cactus-pangenome` in 2.6.4. I'm using the Docker container via Singularity/Apptainer. The same command was working with `cactus-pangenome` in 2.5.1.
```bash
cactus-pa…
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Dear odgi team,
I have used the BubbleGun algorithm recently published to determine the number of bubbles and superbubbles in a pangenome graph of a LAB bacteria.
The command I have used to calc…
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Dear Dr. Ebler,
when I ran the pipeline using the human hprc-v1.1 MC_graph VCF (hprc-v1.1-mc-chm13.vcfbub.a100k.wave.vcf.gz) and GFA (hprc-v1.1-mc-chm13.gfa), I encountered an exception during the …
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Hi,
I conducted a Cactus alignment of 30 mammalian genomes. I want to obtain a sequence similar to Pangenome, which contains insertions of all species. I want to convert the genome coordinates of e…
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This is a second generation version of [Issue: Decide on Technology Stack](https://github.com/graph-genome/graph_summarization/issues/1). Now our requirements have changed significantly. For product…
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Hi
I failed to convert GFA (created by [nf-core/pangenome](https://github.com/nf-core/pangenome)) to rGFA with `gfa2rGFA.py` script from this project.
```
> cat panGraphViewer/panGraphViewerWeb/r…
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Hi
Two features which I think would be really useful in sequenceTubeMap are:
1. On hover over a node or path more information is displayed i.e. all paths passing through the node and the sequenc…
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I have tried to fix this but looks like funannotate compare needs .faa files that doesnt recognise even when I place them in the same directory
/pangenome_out# more funannotate-compare.log
[08/22/…