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Hi,
I was trying to run pggb on a data set, and installed it using bioconda.
However, when I tried to run it, I got the following error:
```
Flag could not be matched: 'S'
smoothxg {OPTIO…
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**1. What were you trying to do?**
Inject a sam file into gam format. The sam file is the output of minimap2 mapping against the output of `vg paths -F` so the paths in the sam file ought to be e…
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Hi,
I am trying to use minigraph-cactus. And I'm not sure how to get the .xg file. The pipeline of D. Melanogaster Pangenome Methods can be seen below.
"cactus ./js 16-fly-pg-2022-05-26-seqf…
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Hi,
Thanks for your work on this program. The method seems really elegant and we've had some really exciting results from it so far.
Here is a brief outline of our preliminary analysis:
- We…
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**1. What were you trying to do?**
I was trying to create a gsca index of a graph created with pggb.
**2. What did you want to happen?**
The index to be created successfully (as happened…
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Hi,
I would like to run odgi heaps on various subsets of samples in my graph, as opposed to running it for the full set of samples -- is this possible without having to generate new graphs altogeth…
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I believe that during graph construction, pggb produces edges that are not covered by any path. If this is in fact the case, then these additional edges can potentially cause false positives in subseq…
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Hello,
I'm trying to make a complete pangenome graph using the --gfa full option.
I previously ran the command without this option, only with "--gfa", and it worked perfectly.
But with the option…
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# nf-core/pangenome feature request
Hi there!
## Describe the solution you'd like
Integrate the [pangenome graph evaluator _`pgge`_](https://github.com/pangenome/pgge).
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I ran Panaroo on my dataset of bacterial genome assemblies. When I visualize the graph in Cytoscape I see many COGs that appear as individual nodes unconnected to anything else. How can I interpret th…