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Hi Gerry,
I wonder if you could incorporate the "colapse_paralogs" step to the merging function. After merging, I find many issues when having paralogs in one of the merged pangenomes. It looks like …
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Just wonder if MicrobeAnnotator can be combined with results from pangenmoe pipeline?
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I created a pangenome graph using pggb, resulting in gfa and og files. I now wish to perform some mappings to the graph and have a few questions:
1. From the pggb documentation I understand that the …
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Hi
I've just ran a cactus-blast job, based on the cactus-prepare output, using the following command:
```
cactus-blast /cactus/jobStore /data/pangenome_cactus/steps-output/pangenome_guidetree.t…
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Hi,
I'm using cactus-minigraph following the workflows of pangenome: https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md
The single reference haplotype is about 800M…
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Hello,
I have created a pangenome of the subset of my (mammalian) data with minigraph-cactus, but I have a larger amount of edges and nodes than I would expect. I have 1,743,464 nodes and 2,386,085…
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Hello,
As an experiment, I've tried take the vcf of the draft human pangenome, use bcftools +setGT to unphase the pangenome vcf, and then rephase the vcf using different reference panels. I am usin…
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## Failed `sanitize_fasta_header` jobs with `sqlite3.OperationalError: disk I/O error` in Cactus Pangenome on WSL Ubuntu 20.04
### Issue Description
I'm encountering an issue with Cactus Pangenome…
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Hello, I tried using the ```PanVizGenerator()``` on the example pan genome (```Pangenome.csv```) and my own pangenome with EC & GO terms, however when I open the ```PanViz.html``` file, I can only see…
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Hi,
I've generated the graph VCF (results/multisample-vcfs/graph-filtered.vcf) from assemblies by running the [pangenome-graph-from-assemblies](https://bitbucket.org/jana_ebler/pangenome-graph-from…