gempasteur/integron_finder repository overview

⁠Integron Finder

Finds integrons in DNA sequences

You can use it in command line, see installation below, or you can use it online on the Galaxy Pasteur⁠.

See Documentation for how to use it:

⁠how to use integron_finder container with docker

The computation are perform under IF user in /home/IF inside the container. So You have to mount a directory from the host in the container to exchange data (inputs data, and results) from the host and the container. The shared directory must be writable by the IF user or overwrite the user in the container by your id (see example below)

mkdir shared_dir
cd shared_dir
docker run -v $PWD:/home/IF  --user $(id -u):$(id -g) integron_finder:<tag> --local-max --circ --keep-tmp NZ_CP016323.fna

⁠how to use integron_finder with Apptainer (formely Singularity https://apptainer.org/news/community-announcement-20211130/⁠ )

As the docker image is registered in docker hub you can also use it directly with Apptainer. Unlike docker you have not to worry about shared directory, your home and /tmp are automatically shared.

apptainer run -H ${HOME} docker://gempasteur/integron_finder:<tag>  --local-max  --circ --keep-tmp NZ_CP016323.fna

or use -b option if the data is not in your home.

apptainer run -H ${HOME} -b <the directory containing data> docker://gempasteur/integron_finder:<tag> --local-max --circ --keep-tmp NZ_CP016323.fna

⁠Output :

By default, integron_finder will output 3 files under Results_Integron_Finder_mysequences:

• mysequences.integrons : A file with all integrons and their elements detected in all sequences in the input file.
• mysequences.summary : A summary file with the number and type of integrons per sequence.
• integron_finder.out : A copy standard output. The stdout can be silenced with the argument --mute

The amount of log in the standard output can be controlled with --verbose for more or --quiet for less, and both are cumulative arguments, eg. -vv or -qq.

Other files can be created on demand:

• --gbk: Creates a Genbank files with all the annotations found (present in the .integrons file)
• --pdf: Creates a simple pdf graphic with complete integrons
• --keep-tmp: Keep temporary files. See Keep intermediate files for more.

⁠Galaxy

You can use this program without installing it, through the pasteur galaxy webserver instance:

• Galaxy Pasteur⁠

⁠Licence:

• Integron Finder is developed and released under open source licence GPLv3⁠ (see COPYING file)
• NCBIfam-AMRFinder is provided by NCBI and accessible here: https://ftp.ncbi.nlm.nih.gov/hmm/NCBIfam-AMRFinder/2021-06-01.1/NCBIfam-AMRFinder.LIB⁠
• The other data files:
  • attc_4.cm
  • integron_integrase.hmm
  • phage-int.hmm
    are licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License⁠

⁠Citation

The paper is published in Nucleic Acid Research.

Identification and analysis of integrons and cassette arrays in bacterial genomes Jean Cury; Thomas Jove; Marie Touchon; Bertrand Neron; Eduardo PC Rocha Nucleic Acids Research 2016; doi: 10.1093/nar/gkw319⁠

Please cite also the following articles:

• Nawrocki, E.P. and Eddy, S.R. (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29, 2933-2935.
• Eddy, S.R. (2011) Accelerated Profile HMM Searches. PLoS Comput Biol, 7, e1002195.
• Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W. and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.

and if you use the function --func_annot which uses NCBIfam-AMRFinder hmm collection :

• Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860 PMID: 29112715