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Hi I've been following this tutorial to evaluate VCF from PGGB: https://pggb.readthedocs.io/en/latest/rst/tutorials/small_variants_evaluation.html#
I get an error at the ```rtg vcfeval``` step, com…
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Hello
I am working on a clonal organism but we believe more and more it might not be so clonal. We have HiFi data and I want to use them to detect MAF. Is it possible with DeepVariant to detect tha…
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**1. What were you trying to do?**
My aim is to split the graph in chromosomes (ideally) so that I can visualize them in `Bandage`
**2. What did you want to happen?**
I was expecting the foll…
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Hi,
I'm trying to use the minigraph-cactus pipeline to build a pangenome graph using 21 fasta files (1 haploid genome + 10 diploid genomes) all of the same species. I'm running the program on my in…
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Hi, I a using the "merge" option of panaroo to combine two pan-genomes created from two datasets. However, when I see the results, some sequences from both pan-genomes that are >98% identical (same le…
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Hello,
I ran `pggb` (`v0.4` from conda) to build a multispecies pangenome (see #226 for details). The command I used was the following:
```bash
outdir="out"
idt="85"
nhaps="8" ## 7 genomes,…
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Hi,
I'm using the PPanGGOLiN for visualizing physical location of gene families. I tried to make light_gexf networks using Gephi with 3 different datasets, and I find out that one of light_gexf fil…
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Hello folks
Thanks for what looks like a very promising method. I'm attempting to create a PanRG from aligned genes from orthofinder across a ~30 sample pangenome (i.e. 30 annotated genome assembl…
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Hi,
I've built a graph with cactus pangenome pipeline and wanted to visually compare with pggb using odgi viz. However, in the cactus pipeline, other than the reference contigs paths stored as P-line…
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Hi
I am interested in merging individual pan-genomes generated for three species (with distinct ANI) within a genus. Is there a recommendation about whether it is okay to split paralogs in order to…