Pangenome analysis

For the pangenome analysis we used orthofinder v2.2.1. All analysis used the output of this tools.

Phylogenetic

For product the phylogenetic tree we used two script (OG_phylo.py & alnToSnp.py) then we used RaXML v8.2.4.

OG_phylo

This program is used to search for orthologues groupe of core genome single copy and create a consensus for phylogenetic tree. For create a consensus, this script align and clean each orthogroups select with translatorX.

Mandatory installation

Arguments take by OG_phylo

  • -g, –group (type : string) : path of the result of orthofinder (format txt)

  • -c, –count (type : string) : path of the count result of orthofinder (format csv)

  • -f, –fasta (type : string) : path of the fasta which contains all sequence of all strain used for orthofinder

  • -o, –outdir (type : none) : path of output directory for all output file

Exemple:

cat /homedir/user/work/directory_input_orthofinder/*.fasta > /homedir/user/work/all_sequence.fasta
OG_phylo.py -g /homedir/user/work/output/Orthogroups.txt -c /homedir/user/work/output/Orthogroups.GeneCount.csv -f /homedir/user/work/all_sequence.fasta -o /homedir/user/work/output/phylo/

AlnToSnp

This Programme is used to keep only SNP from a alignement

Mandatory installation

Arguments take by alnToSnp

  • -a, –alignement (type : string) : path of the count result of orthofinder (format csv)

  • -t, –type (type : string) : Alignement type (ex : fasta)

  • -o, –output (type : none) : path of output file

Exemple:

OG_phylo.py -a /homedir/user/work/output/phylo/sequence_merge.fasta -t fasta -o /homedir/user/work/output/sequence_aln.fasta

Correction_blast

For each orthogroup, the script checks if all isolates absent of orthogroup isn’t a false absence. If this isn’t the case, the script corrects the gene.count file generated by orthofinder.

  • -d, –directory (type : string) : path of the directory which contains all OG fasta file

  • -c, –count (type : string) : path of the count result of orthofinder (format csv)

  • -db, –database (type : string) : path of the all assembly merge file with scafold name : Souche_Scaffold_1

  • -o, –outdir (type : string) : path of output directory for all output file

Exemple:

OG_phylo.py -g /homedir/user/work/OG_fasta/ -c /homedir/user/work/output/Orthogroups.GeneCount.csv -db /homedir/user/work/all_scaffold.fasta -o /homedir/user/work/output/phylo/