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Hi!
We built a graph using 30 samples and mapping the other 1000 samples to the graph using `VG Giraffe`. I think `VG Augment` could add some of the variation from these 1,000 samples to the graph. …
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Hello,
I have used `giraffe` for alignment using:
```
vg autoindex --workflow giraffe -g chr1.gfa -p pangenome
vg giraffe -H pangenome.giraffe.gbwt -g pangenome.gg -mpangenome.min -d pangenome.d…
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@jmonlong says we use `vg add` for some structural variant graph stuff.
Looking at the code, `vg add` does not appear to create paths for the alleles of the variants it adds.
This means we can't…
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Hi
In the Cactus paper (https://www.biorxiv.org/content/10.1101/730531v3) it mentions that it expects the input genomes to be soft-masked. I was wondering how Cactus treats the soft-masked regions.…
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Hi
I've ran the final join step on a large 76 pangenome graph with a maximum of 2TB RAM resource compute node and the job failed due to memory limits going beyond 2TB, to around 2.1TB. Is there a w…
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Is it possible to use GSAlign to align multiple genomes with each other? Say by concatenating the genomes and using the same file as the reference file and the query file? I know in your paper you rul…
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Hi
While running vg autoindex I get complaints about the sequence length being too long. I had the same problem when running vg gbwt, so I set the buffer size to 1000.
Could the same parameter b…
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Hi
I'm trying to load my GFA file, but I'm getting an error.
```
gfaestus *.smooth.gfa *.smooth.chop.og.lay
loading GFA
loading GFA with 734 nodes, 1003 edges
adding nodes
adding edges
add…
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Hi
I'm interested in using BioGraph to linearise a GFA file produced by PGGB (https://github.com/pangenome/pggb) for visualisation in Panache (https://github.com/SouthGreenPlatform/panache). I'm cu…
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I used `cactus-pangenome` (Cactus v2.7.2) to make a graph with two samples supplied to `--reference`, and then used Giraffe to align Illumina reads to the clip graph and surject to the non-backbone re…