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Commit 45f5b54a authored by Amandine  PERRIN's avatar Amandine PERRIN
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Add commands for example

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# With prokka
PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prokka -l Examples/input_files/list_genomes.lst -n EXAM --l90 3 --nbcont 10
# With prodigal
PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prodigal -l Examples/input_files/list_genomes.lst -n EXAM --l90 3 --prodigal --small
# Only QC
PanACoTA annotate -d Examples/genomes_init -l Examples/input_files/list_genomes.lst -r Examples/2-res-QC -Q
# With prokka
PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prokka -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --nbcont 10
# With prodigal
PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prodigal -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --prodigal --small
PanACoTA pangenome -l Examples/1-res-Annotate/LSTINFO-list_genomes.lst -n EXAMPLE4 -d Examples/1-res-Annotate/Proteins -i 0.8 -o Examples/2-res-pangenome
PanACoTA corepers -p Examples/2-res-pangenome/PanGenome-EXAMPLE4.All.prt-clust-0.8-mode1_2019-02-12_13-25-01.tsv.lst
PanACoTA pangenome -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3 -d Examples/2-res-prokka/Proteins -i 0.8 -o Examples/3-pangenome
PanACoTA align -c Examples/3-coregenome/PersGenome_PanGenome-EXAMPLE4.All.prt-clust-0.8-mode1_2019-02-12_13-25-01.tsv.lst_1.lst -l Examples/1-res-Annotate/LSTINFO-list_genomes.lst -d Examples/1-res-Annotate/ -o Examples/4-Algn -n EXAMPLE4
# core genome
PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1_<date>.tsv.lst -o Examples/4-corepers
# strict persistent at 95%
PanACoTA corepers -p Examples/3-pangenome/PanGenome-GENO3.All.prt-clust-0.8-mode1_<date>.tsv.lst -o Examples/4-corepers -t 0.95
PanACoTA align -c Examples/4-corepers/PersGenome_<pangenome-filename>_1.lst -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/2-res-prokka -o Examples/5-align
PanACoTA tree -a Examples/4-Algn/Phylo-EXAMPLE4/EXAMPLE4.grp.aln
PanACoTA tree -a Examples/5-align/Phylo-GENO3_1/GENO3_1.grp.aln -o Examples/6-tree
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