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Make a "quick start" section in the main README file and move demonstrations of more complicated analyses to a GitHub wiki.
Example of a more complicated analysis to explain in the wiki: creating …
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Hi, I ran cactus-pangenome pipeline with `--binariesMode local` on server, the pipeline exited because of `bgzip` error.
> [2023-07-01T02:40:58+0800] [MainThread] [I] [toil.leader] Finished toil ru…
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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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Hi,
Is it possible to visualize the pangenome graph of minigraph output using pgr-tk toolkit?
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Hi
I have a genome graph from Minigraph-cactus I'm trying to create a spliced graph from along with indexes to run vg mpmap with and later rpvg.
I tried running with the GBZ graph directly from …
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Hi Gerry,
I wonder if you could incorporate the "colapse_paralogs" step to the merging function. After merging, I find many issues when having paralogs in one of the merged pangenomes. It looks like …
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Great program! However, when I try to layout my data, the MDS plot falls underneath the pangenome plot.
 your `gfautil` to convert the format, but when I run t…
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Algorithms/tools:
- [x] ~~antiSMASH~~
- [x] ~~[anvio](https://github.com/merenlab/anvio/blob/master/anvio/panops.py#L960)~~ (requires pangenome generation, leaving it out for now in favor of MCL, th…
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Hi,
I have been trying to use gpu-accelerated odgi-layout command, but running the command as outlined in README leaves me hanging with no output, even with a -P flag. After several minutes, I see …