PhageOrder v0.0.2

• The python script (phage-order.py) will run a docker container to reorder and annotate phage genomes.
• It takes
• The input directory must contain fasta formatted sequences with the file extension '.fasta', everything else will be ignored.
• A log file is produced of each run. An example of this can be seen :

This is useful to compare multiple genomes, which are often uploaded 'as is' once the assembly has been complete. However, assembly is random (more information on this elsewhere...) and reordering genomes is not such a trivial task. Especially when many genomes are compared to one another using visual metrics.

Unordered genomes are very likely to lead people to beleive that genomes are less related than they actually are.

As an example:

The image below depicts three publicly available Pseudomonas genomes:

This next image are the same three genomes, but reordered so they begin with the terminase subunits on the forward coding strand.

Image details:

• Pseudomonas phage Kara-mokiny_1: GenBank: OP314870.1
• Pseudomonas phage Chunk GenBank: MT119376.1
• Pseudomonas phage Pa-A GenBank: MN871454.1

These images are not produced as part of this software

To increase the number of ordered phages in public repositories, and make comparisons easier, PhageOrder will reorder the genome based on the small terminase subunit if it can be found. If not it will use the large terminase subunit.

If there is neither, or more than 1 of both, then the genome will be left alone. This container will not change your RAW files.

Citation:

If you use this software please cite below and look at the third party software to cite the correct Prokka and the PHROGS database this container uses.

PENDING

Installation

Install using pip

pip install PhageOrder==0.0.2

Run the command directly

phage-order.py --input <INPUT DIR> --output <OUTPUT DIR>

Run the docker container directly

docker pull iszatt/phageorder:0.0.2

Run the docker image using:

docker run -v <PATH TO INPUT DIRECTORY>:/lab/input -v <PATH TO OUTPUT DIRECTORY>:/lab/output iszatt/phageorder:0.0.2 /lab/bin/annotate.sh

Output

• Reordered genome based on the small or large terminase subunit (hierarchy: small>large)
• Annotations using prokka and the PHROGS database (see third party software below)
• Proteins file produced using the PHROGs index directly from: https://phrogs.lmge.uca.fr/
• Log file

Third-party software

Software	Version	Description	Please cite
prokka	1.14.6	Annotation software designed by Torsten Seemann	https://doi.org/10.1093/bioinformatics/btu153
PHROGS database	1st May access	Database of proteins organised into orthologous groups	https://academic.oup.com/nargab/article/3/3/lqab067/6342220
Biopython	1.79	A set of tools written in python for biological computation	https://biopython.org/

Docker tags

https://hub.docker.com/r/iszatt

License

GNU AGPLv3