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Hello,
I've been playing around with using halPhyloP to compute PhyloP scores on the 447-way placental mammal alignment. Rather than computing PhyloP scores for entire genomes, we would like to co…
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Hi,
The gtdb_to_ncbi_majority_vote.py is great but is subject to biases when multiple genomes are incorrectly annotated on the NCBI.
Have you considered implementing more complex rules such as:
…
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Hi Shujun,
Another question. I'm running panEDTA on a bunch of species. It says it's successfully reannotating the structurally annotated TEs, e.g.:
> Sat Oct 14 15:10:05 EDT 2023 EDTA final …
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As an alternative for subsampling the genes to show in each node I would like to have a possibility to color the node according to its relative density (the number of genomes in each node).
Is it…
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in theory, as we sequence more and more microbial genomes, charcoal should become better and better (balanced a bit by database size and the potential need to dereplicate through species clusters)
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Hi Robbie,
This is my first time using QUILT, so I apologise if these are naive questions. I am in the first step, preparing and reformatting the reference panel. I would like to do that for each ch…
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I am working with large number of genomes (BAM files). I have noticed that BRASS greatly reduces its recall performance on inversions once it passes a certain "threshold" of variants. This only happen…
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We need to review what https://nf-co.re/sarek can do to determine:
- if it could be used as is
- if it could be used with modifications
- if we'd rather extract and replicate some functionality h…
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Hi @davised
So I tried downloading some genomes classified as "Agrobacterium rhizogenes". However, I see that other genomes are also downloaded, including those of Bacillus, Enterococcus, Leptospi…
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Leftover issues and more from #21.
- [ ] Dry runs/test builds are not currently supported. For that we'll need the script to automatically delete all the histories it created during the run. So the…