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Greetings I'm running a syteny analysis on multiple genomes.
#Context: I'm studying the overall synteny among multiple assemblies of a eukaryotic organism, First I took 1 assembly of each species an…
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Hi
I have able to successfully get the pan-genome, core genome and accessory genome from our isolates. What I am also interested is getting unique genes from each isolates. I am wondering if there …
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Hello,
I'm currently analyzing a substantial dataset comprising 11,743 genomes of different _Enterococcus_ species, including over 20 outgroup genomes from the same family and order. because of the…
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I am trying to run query_pan_genome
roughly like this:
query_pan_genome -g clustered_proteins -o output.txt -a difference -i 1.gff,2.gff -t 3.gff
I also tried replacing the -i and -t with --inpu…
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## About the dataset
We have two datasets, one with 8046 _Pseudomonas_ genomes, and
another, a subset of the first, with 6347 _Pseudomonas aeruginosa_ genomes.
For the issues described here we wi…
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I am sorry about this question, because I know somebody asked this issue before, and the answer was the checking the directory.
But, I can not run the "query_pan_genome" properly.
I checked the …
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Dear Roary author and support team:
I use a RHEL 7.9 server to test Roary container.
I use command 'docker pull sangerpathogens/roary' to acquire an image "docker.io/sangerpathogens/roary "
In…
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I want to represent the presence/absence matrix of the pangenome with the newick tree using gheatmap. I want presence in black and absence in white:
```
pangenome
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Hi Dr Horesh,
Firstly, thanks for developing this tool, it’s a really neat way of categorisating the accessory genome, and very useful and usable.
When first trying out the script, I noticed tha…
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Question 1: Do we want to map the contigs or reads against the reference genomes?
Simone: Yes, I think that this is necessary for a number of things, including identification of core and accessory ge…