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Hi.
Now I have the `.gbz` graph file, and I want to simulate the third-generations `long reads` data from a pangenome graph. Can VG simulate the third-generations long reads? Or if there is some m…
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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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We should capture the metadata on workflows somehow. As per @LLTommy's suggestion
https://docs.dockstore.org/en/develop/advanced-topics/best-practices/best-practices.html
Make sure each CWL work…
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Interest have been expressed about visualizing graphs from pggb into Panache ( cf nf-core/pangenome#197), but the steps to convert formats are currently unclear.
Some documentation highlighting how…
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Hi there @anialisiecka,
I am applying ALIBI to a chr20 human pangenome graph https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/scratch/2021_11_16_pggb_wgg.88/chroms/chr20.pan.fa.a2fb2…
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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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Hello,
My input file is the result of `minigraph` , the ekg recommend [https://github.com/vgteam/vg/issues/3129#issuecomment-746383277](url) your `gfautil` to convert the format, but when I run t…
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Hi!
I'm having an issue with wfmash, I cannot run it all. Launching it gives me:
```
(test-env) msgro@devuan:~$ wfmash
Illegal instruction
```
I've tried installing it from bioconda since I ne…
msgr0 updated
2 months ago
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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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A tree can be considered as pangenome metadata. Provide a method to add a `phylo` object to the pangenome (with `$add_metadata()`, and make other methods be aware of it so the can use them to improve,…