sanger-pathogens Roary issues

sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis

http://sanger-pathogens.github.io/Roary

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issues

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Cloud not obtain clear phylogenic tree

#621 Ronykumawat opened 1 week ago
0
The number of pan-genes in gene_presence_absence.csv is less than each genome

#620 Amilycd opened 1 month ago
0
How are genes with frameshift mutations/INDELS handled?

#619 sydelstan opened 2 months ago
0
Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl5/5.34/Encode.pm line 70.

#618 charlesshirima opened 2 months ago
0
Order of genes in alignment

#617 BlabOaklandU opened 2 months ago
0
Roary grouping genes that don't meet similarity threshold (using `-i 100`, and `-s`)

#616 LijMeh opened 3 months ago
6
How can I discover the genetic sequences that are used to group groups in roary?

#615 Deblusantos opened 3 months ago
0
Issue with "Error: Cant access the groups file: clustered_proteins"

#614 wayne1215 opened 4 months ago
1
The singularity image pulled from docker://sangerpathogens/roary does not accept input gff files

#613 dawnmy opened 4 months ago
0
cann't install roary 3.13 with mamba/conda

#612 dawnmy opened 4 months ago
0
core_alignment.aln has lower and uppercase in sequences

#611 samuelmontgomery opened 4 months ago
0
i cant install Roary by mamba

#610 leech1225 opened 5 months ago
2
roary_plots.py heatmap coregenome matrix empty

#609 yjjj2002 opened 5 months ago
0
Cant open file: 14L9VpZJtx/DNA16.gff.proteome.faa Please, help with this issue

#608 alanxelena opened 6 months ago
0
Missing proteome.faa files

#607 sydelstan opened 6 months ago
0
No newick file

#606 Dabiguina94 opened 7 months ago
0
how can i solve this issue

#605 ryujinyuna opened 7 months ago
0
Number of conserved genes increases through genomoes

#604 PauObregon opened 8 months ago
0
Strange Ouput

#603 ShuyiF opened 9 months ago
2
number of conserved/unique genes.Rtab

#602 kimTina321 opened 9 months ago
0
EXCEPTION: Bio::Root::Exception ------------- MSG: Failed validation of sequence '1'. Invalid characters were: ''''''''''

#601 Psedhai opened 10 months ago
0
Cant open file: _clustered.clstr

#600 albbaous opened 1 year ago
2
change the labels of the roary plots

#599 saras224 opened 1 year ago
0
GFF3 file by Bakta

#598 ryu1013 opened 1 year ago
0
Tutorial problem "'GCA_000008285.1_ASM828v1_genomic.fna' is not a readable non-empty FASTA file"

#597 Turnerathopedotedu closed 1 year ago
0
Gene subset from table

#596 canarioviana opened 1 year ago
0
kraken

#595 zzzapperant opened 1 year ago
1
MCL clustering

#594 mweberr opened 1 year ago
0
Compilation Failed

#593 jhill4796 opened 1 year ago
0
Roary needs Rscript 3 or higher Please upgrade and try again

#592 jhcuarta opened 1 year ago
1
Problem with windows wsl and prokka

#591 Bjiornone opened 1 year ago
0
Parameters for Nanopore (ONT) long-reads sequence data

#590 m-ocejo opened 1 year ago
0
Roary won't install in Conda/Mamba python 3.10 environment, does work in python 3.7

#589 dutchscientist opened 1 year ago
0
Use of uninitialized value in require at /Users/.....darwin-thread-multi-2level/Encode.pm line 61

#588 peflanag opened 1 year ago
1
Roary using large dataset

#587 MenusGarg opened 1 year ago
0
MSG: Got a sequence without letters. Could not guess alphabet

#586 augustkx closed 1 year ago
0
installation seem to be stuck

#585 azat-badretdin opened 1 year ago
3
Get a wrong core_gene_alignment.aln

#584 augustkx closed 1 year ago
1
Roary not working

#583 KFWins2022 closed 1 year ago
5
core_gene_alignment file only seems to have 2 of 21 samples

#582 Barrington-wustl closed 1 year ago
1
Question about the fasta cluster iteratively

#581 bucongfan closed 1 year ago
1
Should assemblies be removed if core gene alignment shows redundancies?

#580 chahatupreti closed 1 year ago
1
Error: Cant access the groups file: clustered_proteins

#579 ryu1013 opened 1 year ago
2
wrong indentation output file "gene_presence_absence.csv"

#578 sekhwal opened 1 year ago
0
Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl5/5.34/Encode.pm line 70.

#577 RightCake1 opened 1 year ago
8
core gene alignment timeout

#576 snogu opened 1 year ago
0
roary_plots.py - PDF heatmap blurs edges where png does not

#575 alanbeavan opened 1 year ago
1
I couldn't find specific predicted coding regions in gene_presence_absence.csv.

#574 huminfo8 opened 2 years ago
0
What configuration do I need for the server?

#573 chen202101 opened 2 years ago
0
Problem with running Roary/Blast error

#572 GM110Z opened 2 years ago
0