Roary

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roary and cd-hit

1

I want to know how to remove redundant genes from pan-genome, I analyzed 100 genomes by roary software and got pan_genome_reference.fa file which contains all core and auxiliary genes, I...

zhichusun

Group Naming Convention | Question

2

Hi, Quick query on how Roary assigns names to each cluster. I notice that in my analysis (default settings), I get a number of clusters named as the same gene...

JDHarlingLee

Hello, I have this file in the output folder. But there is no description of it in tutorial. How was it produced? core_gene_alignment.aln + FastTree? Best regards, Valery

valery-shap

NCBI annotated sequence use as input of Roary

1

NCBI sequence (.fna) and gene annotation file (.gff) downloads using curl --remote-name --remote-time ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/192/045/GCF_000192045.2_ASM19204v3/GCF_000192045.2_ASM19204v3_genomic.fna.gz These two files was merged to create a gff3 file using cat genome.gff genome.fna > genome1.gff...

manoj044

MSG: Got a sequence without letters. Could not guess alphabet

2

dhiru16

How to calculate Heaps Alpha value from the roary pangenome analysis ?

3

I have performed the bacterial pangenome analysis using your pipeline. But, I do not know how to obtain/calculate the Heaps Alpha value from the analysis result, to know the pangenome...

dineshkumarsrk

how to extract the sequence of core gene or accessory gene after running roary

2

hello, I ran the roary and wanted to extract the sequences of the core genes or accessory genes in order to annotate them. But I wonder how to extract the...

cylcheyanlin

Bio::Roary::CommandLine::Roary module not installed

1

According to the solution you suggested, I run the $ cpanm -f Bio::Roary and some modules are not installed. Here is the information. --> Working on Bio::Roary Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.13.0.tar.gz ......

cylcheyanlin

_clustered.clstr file does not exist, cannot be read

2

I am using the latest version of Roary (v3.13.0) with cdhit 4.8. But I still get this issue "_clustered.clstr file does not exist, cannot be read" and the warning "perl:...

Haley-Wami

Can't locate Bio/Roary/CommandLine/Roary.pm in @INC

15

Dear all Roary is not working after installing on osx through miniconda3 I have to say that I had also issues while installing Prokka but that has been solved by...

beudes