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Add available SARS-CoV-2 data to the pipeline
- [x] @alexsign to produce GPI file
- [x] add to NEO (change config line in Makefile)
- [x] @alexsign to produce GAF/GPAD (this will be mostly interp…
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Hi,
I was running the SqueezeMeta pipeline to create bins of each sample. All of them were running sperarately and by trying to combine the tables of each sample from a separate folder finally to jus…
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Hello,
I am referring to section 4.9.4 estimation of the core/pan-genome size by sampling genomes. I created the estimated core genome size graph for 4 species. However, there appears to be core g…
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For some odd reason, my heat capacity disappears when I save until I add or remove something from the heat grid. Sometimes all my heat capacity disappears, and some times only part of it.
RimPy Modl…
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Hello fwhelar,
Thank you very much for a great software! I just have a couple of questions that I cannot quite find the answer to in the publication.
1. Is it best to remove genomes from the an…
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Dear author,
Thank you for this great tool to detect the recombination events in the bacterial genomes. I noticed that the pipieline "
ReferenceAlignmentGenerator" or "AssemblyAlignmentGenerator" …
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I just ran roary on a set of assemblies annotated by prokka. Got no error messages but the core_gene_alignment.aln was missing from the output.
Here is the output of roary -a:
> $ roary -a
> Please …
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**Versions**
poppunk v2.5.0
pp-sketchlib v2.0.1
**Command used and output returned**
I bash a script file containing:
poppunk --create-db --output PoppunkDB --r-files r-list.txt --external-cluste…
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Hi!
I'm trying to subset the 661k genomes database (https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001421). I know it has a h5 sketchlib file ([661_ppsketch_v1.5.h5](http:/…
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**Submitting author:** @cagret (Clement AGRET)
**Repository:** https://gite.lirmm.fr/doccy/RedOak
**Branch with paper.md** (empty if default branch):
**Version:** v0.1.5
**Editor:** @lpantano
**Revie…