Galaxy |

PPanGGOLiN all (version 2.2.3+galaxy0)

Select genome files:

All the genome files must be of similar format, either all genbank files or all fasta files. Processing of at least 15 genomes files is recommended, a minimum of 2 genomes files is mandatory. Space is not allowed in filename.

Minimum alignment identity:

Minimum alignment coverage:

Number of classes used to partition the pangenome:

If empty value (default), it will be automatically determined. Otherwise, the value needs to be between 2 and 20 and it is advised to set a value of 3. See the link for the documentation in the help section for more details.

Translation table:

Gene family defragmentation:

Add the following pangenome output files in the Galaxy history:

PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either assembled genomic DNA sequences or provided genome annotations. PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene families in persistent, shell and cloud genomes. It integrates both information on protein-coding genes and their genomic neighborhood to build a graph of gene families where each node is a gene family, and each edge is a relation of genetic contiguity.

The ppanggolin all command generates a partitioned pangenome graph with predicted RGP, spots and modules. Please see the documentation on how parameters can be tuned for this command.