beav - a bacterial genome and mobile element annotation pipeline

beav: Bacteria/Element Annotation reVamped

beav is a command line tool that streamlines bacterial genome and mobile genetic element annotation. It combines multiple annotation tools, automating the process of running, parsing, and combining the results into a single easy-to-read output. Annotated features include secretion systems, anti-phage defense systems, integrative & conjugative/mobilizable elements, integrons, prophage regions, amino acid biosynthesis pathways, small carbon metabolite catabolism pathways, and biosynthetic gene clusters. Type VI secretion system (T6SS) vgrG operons are automatically identified. Plasmid origin of transfer (oriT) elements are also characterized.

The beav pipeline also includes several tools and databases that enhance the annotation of plant associated microbes, including phytopathogens and symbionts. Custom bakta databases provide correct gene names and annotations for phytopathogen virulence genes, effectors, and genes important for mutualist symbiosis. Other tools annotate promoter elements such as the pip box, tts box, nod box, tra box, vir box, etc.

An optional Agrobacterium-specific pipeline identifies the presence of Ti and Ri plasmids and classifies them under the Weisberg et al. 2020 scheme. It also annotates Ti/Ri plasmid elements including T-DNA borders, overdrive, virbox, trabox, and other binding sites, and determines the biovar and genomospecies of the input strain. Virulence and T-DNA genes, including opine synthase and transport/catabolism loci, are also correctly named and annotated.

**beav** will generate Circos plot annotating important features for the genome as well as pTi/pRi plasmid (if Agrobacterium specific analysis is conducted). It is also possible to separately run the Circos script.

# **Installation** The **beav** pipeline requires a number of programs and databases be installed. Therefore, it is highly encouraged and recommended to use conda to install **beav** and all of its dependencies. # From conda (Recommended) It is recommended to use either conda with [libmamba](https://www.anaconda.com/blog/a-faster-conda-for-a-growing-community) or mamba to install beav as this will greatly speed up the time solving the environment. instructions for conda: ``` conda create -n beav conda install -n beav beav ``` alternative instructions using mamba: ``` conda create -n beav mamba install -n beav beav ``` The conda environment can then be activated using: ``` conda activate beav ``` # Alternative: From source Clone the beav github repository. ``` git clone https://github.com/weisberglab/beav.git ``` **If installing from source, DBSCAN-SWA, TIGER2, and GapMind (PaperBLAST) need to be installed in the software folder within the beav folder. Then the BEAV_DIR environment variable needs to be set and pointing to the beav directory.** **Prerequisites:** | Program | Install location | | --- | --- | | Bakta | PATH | | IntegronFinder | PATH | | MacSyFinder | PATH | | DefenseFinder | PATH | | TIGER2 | $BEAV_DIR/software | | GapMind (PaperBlast) | $BEAV_DIR/software | | DBSCAN-SWA | $BEAV_DIR/software | | antiSMASH | PATH | | EMBOSS | PATH | | HMMER | PATH | Databases for each of these programs can then be installed manually. Alternatively, the following can be used to install them automatically. # Install all databases ``` conda activate beav beav_db ``` ## Database script optional parameters usage: beav_db [--skip_bakta_db] [--light] [--bakta_db_path DIRECTORY] [--update] --skip_bakta_db Skip downloading the Bakta databases --light Install the light version of Bakta databases --bakta_db_path DIRECTORY Install Bakta databases in nondefault location --update Update Bakta databases # Usage #### NOTE: there is currently a [bug](https://github.com/mdmparis/defense-finder/issues/42) in the latest DefenseFinder models that cause an error in MacSyFinder when running it. We recommend running Beav with `--skip_defensefinder` until the MacSyFinder [bug fix](https://github.com/gem-pasteur/macsyfinder/commit/27ee21ceb8e7100d9183b084356f791487aca4ad) is released in bioconda. Alternatively, copying the patched file to the MacSyFinder python library folder of your conda release will fix the issue.

Patching instructions

To do so, find the python version of your conda environment: python --version Then download the patched registries.py file: wget https://github.com/gem-pasteur/macsyfinder/blob/27ee21ceb8e7100d9183b084356f791487aca4ad/macsypy/registries.py Then copy it to the correct folder in your conda env, changing the python version as necessary: cp registries.py $CONDA_PREFIX/lib/python3.9/site-packages/macsypy/

``` usage: beav [--input INPUT] [--output OUPUT_DIRECTORY] [--strain STRAIN] [--bakta_arguments BAKTA_ARGUMENTS] [--tiger_arguments TIGER_ARGUMENTS][--agrobacterium AGROBACTERIUM] [--skip_macsyfinder] [--skip_integronfinder][--skip_defensefinder] [--skip_tiger] [--skip_gapmind][--skip_dcscan-swa] [--skip_antismash] [--help] [--threads THREADS] [--genbank] [--continue] BEAV- Bacterial Element Annotation reVamped Input/Output: --input, -i STRAIN.fna Input file in fasta nucleotide format (Required) --output DIRECTORY Output directory (default: current working directory) --strain STRAIN Strain name (default: input file prefix) --bakta_arguments ARGUMENTS Additional arguments and database options specific to Bakta --antismash_arguments ARGUMENTS Additional arguments and database options specific to antiSMASH (Default: \"$antismash_args\") --tiger_blast_database DBPATH Path to a reference genome blast database for TIGER2 ICE analysis (Required unless --skip_tiger is used) --run_operon_email EMAIL Annotate predicted operons using the Operon-mapper webserver. Must input an email address for the job Options: --agrobacterium Agrobacterium specific tools that identify biovar/species group, Ti/Ri plasmid, T-DNA borders, virboxes and traboxes --skip_macsyfinder Skip detection and annotation of secretion systems --skip_integronfinder Skip detection and annotation of integrons --skip_defensefinder Skip detection and annotation of anti-phage defense systems --skip_tiger Skip detection and annotation of integrative conjugative elements (ICEs) --skip_gapmind Skip detection of amino acid biosynthesis and carbon metabolism pathways --skip_dbscan-swa Skip detection and annotation of prophage --skip_antismash Skip detection and annotation of biosynthetic gene clusters --continue Continue running BEAV from any point in the pipeline. Rerun programs that gave an error or were skipped. --gbk Use a GenBank file as input General: --help, -h Show BEAV help message --threads, -t Number of CPU threads ``` # Options **--antismash_arguments** Additional antiSMASH arguments can be input into antiSMASH using the --antismash_arguments option. This allows for full usage of antiSMASH and additional databases. **--tiger_blast_database** Required if running TIGER. Users must provide a path to a blast database of reference genomes using the --tiger_blast_database option. **--bakta_arguments** Additional arguments can be passed to bakta using the --bakta_arguments option. **--agrobacterium** The --agrobacterium option activates an additional pipeline to provide agrobacterium-specific annotation. **--skip-PROGRAM** The skip options allow for specified programs to be skipped if the annotation is not needed or required programs are not installed. **--continue** The continue option will check the output of existing Beav runs and rerun programs that errored or were skipped. This option allows for the pipeline to be used with existing Bakta runs. **--gbk** A GenBank file can be used as the input file when the genbank option is used. # Examples **Minimal run** ``` beav --input /path/to/file/test.fna --threads 8 --skip_tiger ``` **Standard run** ``` beav --input /path/to/file/test.fna --threads 8 --tiger_blast_database /path/to/databases/blast/refseq_genomic.fna ``` **Standard run with operon annotation (remote)** ``` beav --input /path/to/file/test.fna --threads 8 --tiger_blast_database /path/to/databases/blast/refseq_genomic.fna --run_operon_email myemail@email.com ``` **Standard run with genbank input** ``` beav --input /path/to/file/test.gbk --threads 8 --tiger_blast_database /path/to/databases/blast/refseq_genomic.fna --gbk ``` **Complex run** ``` beav --input /path/to/file/test.fna --threads 8 --bakta_arguments '--db /path/to/alternative-data-bases/bakta-1.7/' --tiger_blast_database /path/to/databases/blast/allagro.fna --agrobacterium --skip_integronfinder ``` # Standalone Circos plot generation To generate Circos plots on your GenBank file independant of the **beav** pipeline, make sure the beav conda environment is activated: ``` conda activate beav ``` Usage: ``` beav_circos -i [-c ] [--pTi ] ``` Examples: ``` # Generate a general Circos plot for all contigs beav_circos -i test.gbk # Generate a general Circos plot for all contigs and a oncogenic Circos plot for single contig beav_circos -i test.gbk --pTi contig_1 # Generate a general Circos plot for all contigs and a oncogenic Circos plot for a set of contigs beav_circos -i test.gbk --pTi "contig_1 contig_2" # Generate a general Circos plot for single contig beav_circos -i test.gbk -c contig_1 # Generate a general Circos plot for a set of contigs beav_circos -i test.gbk -c "contig_1 contig_2" ``` # Citation Beav can be cited as: Jung J.M., Rahman A., Schiffer A.M., and Weisberg A.J., Beav: a bacterial genome and mobile element annotation pipeline. (2024) bioRxiv 2024.01.25.577299; doi: https://doi.org/10.1101/2024.01.25.577299