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Hello,
I want to build a genome graph based on VCF files of variant information for hundreds of samples.
Below I tested two samples using the following commands:
`gramtools build -o ./gram --…
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for charcoal, there is some interesting logic encoded [here](https://github.com/dib-lab/charcoal/blob/c7fd19205e92461bb5ee09735e05d107e35a1779/charcoal/utils.py#L198) in utils.py --
```
taxlis…
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Dear Pargenes,
Is there a feature in Pargenes that allows you to sort trees by the number of taxa in each tree?
For example, most clustering programs will output single copy core gene alignmen…
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Is it possible to view the hierarchical clustering tree that is created when the tile plots are made? It would be useful to see how some of the groups branched.
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Hi,
Thank you for developing such a really great method and very cool study tool!
I was able to run SMEG through singularity installation and changed download_genomes.sh line 4 to "wget ftp://ftp.…
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### Description of the bug
Hello,
I'm reaching out regarding an intermittent error I've been encountering in my workflow. Specifically, I've observed that on occasion, a particular sample runs smo…
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Hi, I am using the allotetraploid plant species to assemble the genome. I have the 3 cells PacBio HiFi reads data to assemble the genome. I ran the code as given following using hifiasm/0.19.8 versio…
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Hi!
I'm trying to run Binsanity-wf, but I'm getting this error. I suspect something is going wrong after checkm analysis.
This is the command I used:
Binsanity-wf --threads 24 -f ./ -l ./final_…
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Hi @XiaomingXu1995
First, I'd like to congratulate you for RabbitTClust. I spent weeks trying to find a clustering algorithm that worked in the scale I needed and RabbitTClust solved all of my pro…
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## Tasks
1. all PCGs BLAST all-vs-all search - diamond.py
2. gene sets construction
3. real alignments to respective sample contigs specific to gene coordinates
4. module detection of coverage-c…