Roary
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sanger-pathogens
Rapid large-scale prokaryote pan genome analysis
Hi, Thanks for developing this useful tool. I used the -z parameter to keep all the intermediate files. However, when I checked the files, I found that the number of...
Hi! I've been using roary on OSX with no problem but suddenly I got an error ending: "For further info see: http://sanger-pathogens.github.io/Roary/ Combine proteins into a single file" (I know...
Hi there, I am trying to use Roary with an input data of 4500 prokaryotic genomes. After more than a month running, just 5 days before the end of the...
Hi, I have 142 genomes for analysis. And according to the summary, pan-genome has 29208 genes and the core genome has 1482 genes. So I tried to get the gene...
Hello, I ran Roary for 102 E. coli samples (fasta files were from ncbi database and .gff files were created using Prokka) and the command line that I used was...
I have annotated several assmbled plasmids from several isolates using Prokka, and I am attempting to analyse them with roary. I installed roary using conda, added the gff files from...
Dear authors, For Roary inputs, it needs the gff files containing nucleotides sequences. I wanted to know how do you convert nucleotide sequences to protein sequences? Do you use the...
Hi, I ran roary in a macOS catalina and encountered this error: Use of uninitialized value in require at /Users/drbandoy/miniconda3/envs/roary/lib/site_perl/5.26.2/darwin-thread-multi-2level/Encode.pm line 61. Error in library(ggplot2) : there is no package...
Hi, I am trying to run Roary and I am getting this output: ``` $ roary -v -e -z -g 1000000 -f roary_test gffs/SGB_10006.gff gffs/SGB_10028.gff 2020/03/24 09:31:09 PRANK (or MAFFT)...
I tried using Roary on the galaxy server with multiple assembled plasmid sequences (gff files from prokka annotation) using the non-paralog method, but I think I am getting strange results...
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Rapid large-scale prokaryote pan genome analysis