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Hi,
This is about group_size_nuc. For a specific gene, the gene_presence_absence_roary.csv file shows min_group_size_nuc= 489 and max_group_size_nuc= 762. From the gene_calls.ffn, the minimum numb…
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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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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…