Scoary

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I have a set of 100 bacterial genomes. I annotated them with Prokka and performed pangenome analysis with Roary. Roary outputs the core gene alignment file which I then used...

chahatupreti

Significance of the worst_pairwise_p

3

I am interested in finding out how to interpret the significance of a gene where the best_pairwise_p is < 0.05 or lower but the worst_pairwise_p is non-significant. Assuming this gene...

plasmid02

Hi, Thank you for this convenient tool. Are there any way to ignore missing data(- or NA) in genotype data? I converted vcf to present/absent file. Some samples have missing...

snackens

fix ValueError: invalid mode: 'rU' with python3.11

1

Since python3, the universal newline mode 'U' has no effects. Since python3.11, that mode is obsolete and its use raises: Command: scoary.py -g scoary/exampledata/Gene_presence_absence.csv -t scoary/exa mpledata/Tetracycline_resistance.csv -o Test1 --no-time...

emollier

Unrecognized character found in trait file

2

Command: /opt/anaconda3/envs/scoary/bin/scoary -g gene_presence_absence_roary.csv -t Hostgroup_membership.csv -p 1 -c BH --no_pairwise Performing no pairwise comparisons. Ignoring all tree related options (user tree, population aware-correction, permutations). Reading gene presence absence file...

shaodongyan

Appreciate @AdmiralenOla if you could guide me in making the approproate traits file for scoary. scoary seems to read the gene presence absence file accurately. Command: /home/svu/e0512807/miniconda3/envs/scoary/bin/scoary -t traits_scoary_plant_soil.tsv -g...

arijitnus