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Hi! I'm having an issue running main_probabilities.py in my dataset of 60x wgs tumour. It is crashing with the following error:
```
[xalmal@bespin sv-bay-data]$ /apps/CLC_ExternalApps/SV-Bay/minic…
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we are using GTDB taxonomy because -
* GTDB provides a nice collection of representative genomes
* GTDB provides species clusters based on ANI, which matches the approach used in charcoal
* the g…
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In `proteinortho` file, Roary now adds a `Alg.-Conn.` column. It seems to have every gene in the DB. It screws up the pan genome tree, the clustering, and the alignment views.
Deleting that column…
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Dear Kevin,
Since mustv2 runs more than 20 days. I terminated the programme and split the genome, whereupon mustv2 issued the following errors.
Spliting the genome into 10 sub-genomes ... [S…
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Hello Team,
I've been working with pairtree to analyze some of the cancer samples from our cohort data. Since each patient has multiple samples, including primary and recurrent tissues, the resulti…
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Dear CoverM team,
I remember I suggested skani some time ago, and glad to see you included it in the newest version. However, you might notice inaccuracy estimations below 85% ANI. While with the n…
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# Association
- [ ] [A simple, consistent estimator of heritability for genome-wide association studies]( https://www.biorxiv.org/content/biorxiv/early/2017/10/17/204446.full.pdf)
- [x] [Multivari…
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@crimBubble @molbio-dresden
Hope you are well down.
I am trying to use Eccsplorer to find eccDNA from my own data, but get info " No high (potential) confidants eccDNA candidate regions found". Dur…
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- Graph construction was implemented using `rustworkx` in #234, I want to mention that the `rustworkx` python interface is remarkably optimized. Using Python, we can build all graph-downstream analyse…
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I tested Galah on a small and on a large dataset. In both, I get
```
[2022-09-14T07:35:31Z INFO galah::dashing] Running dashing to get approximate distances ..
[2022-09-14T07:35:31Z ERROR bird_t…