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Hi there I'm working on a `LaTex` documents where I'm using several `tcolorbox` code blocks for the BASH language. In one of them I happen to have a parameter for a tool of such form: `0.03`. Apparent…
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Add panphlan modules & subworkflow to pipeline
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Hello,
I find there are a fewer SNP overlap rate between the callset form pangenome-graph-from-assemblies and the GATK results. What could be the reason? The article seems to only compare the abili…
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Thank you for putting together this repository for exhaustive host depletion! I am in the process of setting it up to run on my cancer samples. I noticed that the create_indexes.sh script (in the main…
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Donovan Parks suggested using the full 134k (or more?) GTDB databases in detecting and analyzing contamination, and it's something we should think about evaluating with charcoal. On the other hand, th…
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Hi Erik
I've followed your PGGB updates and am now using smoothxg with added consensus paths. I've put the graph into VG and sequenceTubeMap. I notice I have 8 different consensus paths in my graph…
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Dear all,
I have been having the following issue when installing panX. I followed the steps as in the site and used miniconda as indicated.
`Traceback (most recent call last):
File "./panX.py…
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**1. What were you trying to do?**
I am trying to use vg to extract the non-reference paths from the Minigraph-Cactus (version 2.6.7) pangenome.
I used the command
```
vg paths -S SDTS1 -…
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* Create a new markdown page for records supporting where our data came from
* Coordinate with the #pangenome team on slack. Particularly @ekg who has produced the first GFA with 50 individuals. ht…
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Hi, good day. i have the following problems but my tormes format is generated but with errors.
error reported on command line
"WARNING: Core gene alignment tree was not generated during pangenome …