Galaxy |

Roary (version 3.13.0+galaxy3)

Individual gff files or a dataset collection:

Select between individual gff files or a collection of gff files

select gff inputs to Roary:

Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file.

minimum percentage identity for blastp:

Sets the minimum percentage identity for protein matches

percentage of isolates a gene must be in to be core:

The total percentage of the isolates that must have the gene for it to be considered a core gene.

Additional outputs:

Summary statistics, core gene alignments and Gene Presence/Absence tables are always produced.

Advanced options

Advanced options 0

Roary

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM.

To use Roary, select two or more gff3 files OR a collection of gff3 files

Options:

Minimum percentage identity for blastp - an integer, default is [95]

Percentage of isolates a gene must be in to be core - a float, default is [99.0]

Advanced Options:

Maximum number of clusters - integer, default is [50000]

Don't split paralogs - check box

Translation table - which translation table to use, an integer, default is [11]

Change the MCL inflation value - a float, default is [1.5]

For further info see: http://sanger-pathogens.github.io/Roary/