Roary
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sanger-pathogens
Rapid large-scale prokaryote pan genome analysis
Hello All, I performed a pangenome analysis with roary on a set of data. And I am finding it difficult to interpret the pangenome frequency chart. I checked on the...
Hi , Its my first time running roary and I am trying to understand and roary outputs for my task. My task is to : to find the core genes...
Roary fails to run on GFF files exported from Geneious, while runs perfectly on prokka GFF files. I have compared the files in text editor, they do look different, in...
Hi everyone, I used roary_plots.py and received the three output files, but the file matrix.pgn that gives me the tree didn`t have the name of the strains in each branch....
I've just installed Roary v 3.13.0 via conda and running `roary -a` I get a message > 2021/04/08 16:21:25 Determined cd-hit version is Use of uninitialized value in numeric lt...
Hello, I ran roary and got the necessary files. I downloaded the roary.plots code in a "roary_plots.py" file. I tried running the next line of code: `python roary_plots.py core_gene_alignment.nwk gene_presence_absence.csv`...
I am using roary and a exception appear several times during the execution: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Could not read file 'pan_genome_sequences/rplK.fa.aln': No such file or directory This happens...
Along with, percentage identity cutoff value can we also introduce query coverage cutoff value for forming groups or grouping of core genes across the genomes. Because in some genomes, it...
I find that the "Number of blastp hits with different percentage identity" presented in p.5 of the output file Rplots.pdf could be a simple useful tool to estimate the blastp...
Dear Andrew and Torsten, I am using Roary version 3.13.0, which I installed with conda. I've been computing the alignments with a subset of 24 E.coli samples. However I am...
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Rapid large-scale prokaryote pan genome analysis