-
Remove enforcing of the columns "Non-unique gene name" and "Annotation" in the output. Some users might have input file with only a single identifier column (Gene ID) before sample info starts, and wa…
-
Hello,
Great job on the program - looks very promising!
Unfortunately, I am having some issues implementing treeWAS using ClonalFrameML output. I can load the data just fine using the read.CFML(…
-
Hi Andrew,
I'm running Roary on three genomes, which I annotated with Prokka. Apparently the BLAST steps fails, although the program still finishes. The combined genes from the three genomes end up…
-
Hi,
Thanks for building this tool :-)
Two questions:
1) Is it possible to extract the core genes from a subset of strains, which are absent in the other strains? (the core of the accessory gene…
-
Hi,
I used "query_pan_genome -a difference" to compare 2 samples. I've tried to find a detailed explanation about each *_statistics.csv output column, but I couldn't read anything related to it.
I'm …
-
Dear Devs
When I try to use LS-BSR, an error occur:
`Traceback (most recent call last):`
`File "ls_bsr.py", line 492, in `
`options.filter_scaffolds,options.prefix,options.temp_dir,options.debug)`
…
-
Hi,
I am trying to build a pan-genome from 193 bacterial strains, with increased sensitivity in `cdhitGrouping()` to account for high diversity in the set. However, The grouping fails with a fatal …
-
Hi
I was wondering whether gubbins would be able to accurately detect recombination from a core gene alignment, implemented by Roary?
-
Hello
I have generated a core-genome tree using protein clusters, however, is it possible to generate a pan-genome tree using Roary based on both core and accessory genome protein clusters?
-
I have just installed a new Biolinux8 workstation and included Roary (of course). It installed v. 3.6.5, and when I used it with a known Campylobacter coli test set, it claimed that there were 0 core,…