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Digesting some feedback, I wonder if we should rename to tsbrowse, as this is primarily an ARG browser (like a genome browser, for ARGs)?
That's definitely better than ``tsviz``, which to my mind w…
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I just realised something possibly profound. To a first order approximation let's assume that genomic rearrangements are genealogically "neutral", or more specifically that given two genomes in a GIG,…
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Some brief comments on:
https://github.com/SANBI-SA/combat_tb_model/blob/master/docs/genome_annotation_model.md
Very clearly documented, thank you @thobalose and @pvanheus. The overall strategy make…
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Hello,
Thank you for developing this super useful pipeline. I have two isolates of Agrobacterium species sequenced with ONT. After basecalling, I got 2.2Gb data for one isolate AT1, and 1.2 Gb data f…
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Hi developer,
**Describe the bug**
I meet an error with `03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo.sh`
I attached the log files
[nextDenovo.sh.e.txt](https://github.com/Nextomics…
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Hi,
I am trying to use PanGenie to genotype personalized minigraph-cactus graphs generated by `vg haplotypes`. In the [personalized pangenome paper](https://www.biorxiv.org/content/10.1101/2023.12.…
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**Is your feature request related to a problem? Please describe.**
For multiple genome comparisons, it is quite hard to find a genome browser that can handle it. I know that JBrowse2 can visualise 2 …
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We should change the ARG tutorial to say that _msprime_'s `record_full_arg` is now simply a shorthand for `additional_nodes = msprime.NodeType.COMMON_ANCESTOR | msprime.NodeType.RECOMBINANT`.
Addit…
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## ❓ Questions and Help
Traceback (most recent call last):
File "tools/relation_test_net.py", line 123, in
main()
File "tools/relation_test_net.py", line 105, in main
data_loaders_va…
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Hi,
I'm using a lot panaroo for a research project. I generated a gene_presence_absence matrix from 1500 bacterial genomes.
Then I used this matrix to train a supervised machine learning model. I go…