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Dear Panaroo developers and community,
In the output documentation, it is noted that "to avoid issues with the multi-mapping of reads, paralogous gene clusters will only be represented once in this…
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I have been looking at differences between two almost identical Klebsiella isolates (KN0056A-F and KN0056A-L) in the Pandora vcf output. For several regions in the reference Pandora is suggesting that…
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Hello! I am trying to use phandango for getting a tree against the gene presence absence matrix from Roary. It all worked fine when I had smaller data sets, but now I have more genomes and a larger ge…
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- [x] add metadata to dendrogram
- [x] cpd search feature
- [x] add dendrogram to trait view -> allow recoloring
- [ ] in dendrogram: instead of only gene presence-absence, show gene count!
- [x] …
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I have a couple hundreds of single amplified genomes from single cell assemblies which have low completeness (completeness
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After running Pyseer using
pyseer --phenotypes phenotypes.tsv --pres gene_presence_absence.Rtab --similarity phylogeny_similarity.tsv --lmm --covariates covariates.tsv --use-covariates 2 --cpu 8 >…
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Latest updates were excellent, thanks!
I have a suggestion. After running ABRicate, could it be possible to select % coverage and % identity for the summary report, too? I mean keep results.tab as…
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==== Scoary started ====
Command: /Users/nondumisondhlovu/opt/anaconda3/bin/scoary -g gene_presence_absence.csv -t case.csv -s 15
Reading gene presence absence file
CRITICAL:
Traceback (most recen…
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Hi Gerry,
I get that Panstripe's main goal is to model the gene exchange rates, but would it be straightforward to get an idea of the function of the exchanged genes? I'm thinking of listing annota…
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Hello!
I have recently installed Coinfinder and have been running into issues with getting it to run. Below is the code I am using to run the program.
`coinfinder -i genes_presence_absence_coinf…