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I had a question about contamination and strain heterogeneity. I ran CheckM on around 500 bins from a metagenome. The contamination ranges from 0 to 870.28, and the strain heterogeneity ranges from 0 …
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I am running Cactus with 27 fungal species, and I can't get it to complete. It keeps stopping after giving a message about disk usage and then saying it has jobs waiting to run. I'm on a slurm cluster…
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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…
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**1. What were you trying to do?**
Build giraffe index
**2. What actually happened?**
I got an error
**3. What data and command can the vg dev team use to make the problem happen?**
I tried h…
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I'm on a HPC system with [modules](https://modules.readthedocs.io/en/latest/). I've managed to install with python version 3.8, 3.9, 3.10 but not python3.11.
This is how I attempted installation:
…
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# nf-core/pangenome feature request
Hi there!
## Describe the solution you'd like
Recently, there has been a major `pggb` update https://github.com/pangenome/pggb/pull/46. It improves perform…
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Hi,
Thanks for developing this great tool. I would like to use the "HPRC-CHM13 (88 haplotypes)" variant reference. Based on the name, I think the reference genome I should use for genotyping is CHM…
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Do I need to softmask the input assemblies?
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## Is your feature request related to a problem? Please describe
We don't exploit the possible parallelization of the pipeline when applying sequence partitioning to the input FASTA. A bash imp…
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Hi,
thanks for your efforts with PGGB and odgi first up.
I've generated quite a few graphs in PGGB and am trying to work with them in vg and with graphaligner. In general, I can map short and lo…