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Hello, i have been having some troubles replicating the results from https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/mc-pangenomes/README.md. To be specific, i could not split the…
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Hello,
I used PPanGGOLiN from gbks to do the whole pipeline and now, after an examination of the pangenome, I want to remove some families (so that they are not considered in the rarefaction, RGP, …
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Hi,
I've followed the install instructions and am running a test on my dataset.
I am running with the following command:
```python3 mcclintock.py -r Iterative_pangenome_reveal_map_min10kb_u…
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Hi Glenn and all,
I am not sure if I need to report this issue here or within the cactus repo (as here the latest version is 1.1.3, while the code from cactus 2.6.4 shows vg version 2.2).
`hal2vg …
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@nuzla @ZoeYang2020
Would that be possible for you to provide information for us to create a summary/workflow diagram similar to what we have on this workshop repo for RNA-seq data analysis https://…
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Hi,
How could I provide path coordinates for `panacus` from `pggb` graph? Since it didn't have an interval in the GFA, this function only works for `Minigraph-Cactus` graph?
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Hi
I'm using vg version v1.40.0 "Suardi" packaged along with PGGB version 0.5.3.
I have ran Minigraph-cactus and generated a GBZ graph. The graph is clipped and filtered. I try and generate a sp…
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Dear developers,
Thank you so much for this tool!
I created a pangenome of Arabidopsis following the minigraph-cactus pangenome pipeline. Then, I installed odgi using conda to visualise the pange…
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### Description of feature
The future v0.7.1 release will come with some bug fixes, so this is really required to have.
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I've been enjoying using PPanGGoLiN, thank you for developing this workflow! I have discovered that a locus tag of interest, which can be found in my .gbff file, cannot be found in the sample's projec…