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Execution of Jolytree via by the option `--tree` (see https://gitlab.pasteur.fr/GIPhy/JolyTree)
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JolyTree.sh -i $dirIn -b $dirOut -t $threads
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Execution of integron finder version 2 `--integron` (see https://github.com/gem-pasteur/Integron_Finder)
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integron_finder --cpu $threads --outdir $dirOut --gbk --func-annot --mute $genome
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