Whokaryote uses a random forest classifier that uses gene-structure based features and optionally Tiara (https://github.com/ibe-uw/tiara) predictions to predict whether a contig is from a eukaryote or from a prokaryote.
You can use Whokaryote to determine which contigs need eukaryotic gene prediction and which need prokaryotic gene prediction.
Issues can be created via GitHub: https://github.com/LottePronk/whokaryote
If you have used Whokaryote in your work, please cite our paper:
Pronk, Lotte J U, and Marnix H Medema. “Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure.” Microbial genomics vol. 8,5 (2022): https://doi.org/10.1099/mgen.0.000823
Whokaryote was developed to run from the commandline on a UNIX-based system such as Ubuntu or MacOS. If you want to use Whokaryote on your Windows PC, we recommend you install Windows Subsystem for Linux (WSL). See https://docs.microsoft.com/en-us/windows/wsl/about
You can now easily install Whokaryote via conda (or mamba). Simply use the following command to install Whokaryote in a (dedicated) conda environment:
conda create -c bioconda -n whokaryote whokaryote
Are you new to using conda? You can download miniconda here: https://docs.conda.io/en/latest/miniconda.html
Alternatively, you can install Whokaryote and its dependencies in a conda environment in Windows, see the instructions. You can download miniconda here: https://docs.conda.io/en/latest/miniconda.html
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Make a new and empty conda environment, and activate it:
conda create -n whokaryote python==3.8
conda activate whokaryote
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Install dependencies with these commands:
python -m pip install tiara
(see: https://github.com/ibe-uw/tiara)- download the windows binary of prodigal from the following link: https://github.com/hyattpd/Prodigal/releases/tag/v2.6.3
- change the file name:
move prodigal.windows.exe prodigal.exe
- move the file to the directory from where you run Whokaryote.
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Install Whokaryote:
- Navigate to a directory you want to install Whokaryote in.
- Clone Whokaryote with this command:
git clone https://git.wur.nl/lotte.pronk/whokaryote.git
(orgit clone https://github.com/LottePronk/whokaryote.git
) - Go to the Whokaryote directory:
cd whokaryote
- Install Whokaryote in your (conda) environment with
python setup.py install
Use whokaryote.py --help
to see all the options:
-h, --help show this help message and exit
--contigs CONTIGS The path to your contigs file. It should be one (multi)fasta (DNA).
--outdir OUTDIR Specify the path to your preferred output directory. No / at the end.
--gff GFF If you already have gene predictions, specify path to the .gff file"
--f If you want new multifastas with only eukaryotes and only prokaryotes. This can take a long time.
--minsize MINSIZE Select a minimum contig size in bp, default = 5000. Accuracy on contigs below 5000 is lower.
--model MODEL Choose the stand-alone model or the tiara-integrated model: S or T. Option 'T' only works with argument --contigs
Note: When using Windows, you may need to run Whokaryote from the commandline as follows:
python whokaryote\bin\whokaryote.py [options]
whokaryote.py --contigs contigs.fasta --outdir whokaryote_output --prodigal_file contigs_genes.gff
This is the standard way to run Whokaryote. If you don't specify --model, it will run the model that integrates Tiara predictions. This is recommended.
If you already have gene annotation files (.gff or gene coordinates file from prodigal), use the --prodigal_file option.
If you don't have an annotation file yet, you can use only --contigs and --outdir. Prodigal will then be run on your contigs file, which may take a while.
With the example command, you will get the following output files:
- A file with all contig headers that were classified as eukaryotic (eukaryote_contig_headers.txt), and a similar file for prokaryotic contig headers (prokaryote_contig_headers.txt)
- A fasta file with only contigs that were longer than 5000 bp, called contigs5000.fasta
- A gene coordinates file generated by prodigal called contigs_genes.genes
- A .csv file with all the calculated features called featuretable.csv
- A file with the tiara predictions called tiara_pred.txt
- A .csv file with the calculated features and the predictions called featuretable_predictions_[model].tsv
- A .tsv file with only the contig ID and the predictions called whokaryote_predictions_[model].tsv
Note that contigs with less than 2 genes or shorter than the minimum size are not classified and do not appear in the output.