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Dear odgi team,
I have used the BubbleGun algorithm recently published to determine the number of bubbles and superbubbles in a pangenome graph of a LAB bacteria.
The command I have used to calc…
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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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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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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,…
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Is there a way to generate a joint-genotyped vcf with pangenie? If I understand the software correctly, only the variants in the pangenome reference are called across all the genotyped samples while…
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I'm getting this error (see below). I used ont_fast5_api to demultiplex the multi-fast5s and then ran poreplex on those fast5s. Any input would be helpful. Thank you.
2019-01-31 14:21:01,777 Com…
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I think this issue is related to something that has been mentioned previously here, but I'm not sure that it is resolved.
I am using GSalign to align and call variants from a series of assembled ge…
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We want to be able to load the RASTTk annotations to anvio to compare the annotations used in the model to what Michelle got from the pangenome.
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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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Hello again,
I realized that even though my [issue](https://github.com/pangenome/smoothxg/issues/209) affects `smoothxg`, it is more concerned with an `odgi` algorithm, so I am putting it also here…