PolioPoly

Installation

PolioPoly is simple to use. All of its dependencies and runtime environment has been packed into one Docker image. To run PolioPoly, you just need to install Docker following this instruction.

Once Docker is installed, you can download the command line script poliopoly using following command. Note this script is written in bash which is natively supported by MacOS and Linux. If you are using Windows, you need to install Linux on Windows with WSL for using this script.

sudo curl -sSL -o /usr/bin/poliopoly https://raw.githubusercontent.com/hivdb/poliopoly/main/bin/poliopoly
sudo chmod +x /usr/bin/poliopoly

Usage

A directory of Illumina paired Polio FASTQ files and a primer BED file are required for running the command poliopoly. Replace the following options:

poliopoly \
  -i path/to/fastq/directory \
  -o path/to/output/directory \
  -t S3 \
  -p path/to/primers.bed \
  -n run_name

The options:

-i <input_dir>     input directory which includes paired FASTQ files
-o <output_dir>    output directory
-t <S1|S2|S3>      reference polio serotype
-b <primer_bed>    location of BED file of primers
-n <resume_name>   resume of NextFlow, see https://bit.ly/3xpKmEK

Optional environment variables:

IVAR_VARIANTS_MIN_FREQ    minimum frequency of `ivar variants` (default: 0.75)
IVAR_VARIANTS_MIN_QUAL    minimum quality of `ivar variants` (default: 20)
IVAR_VARIANTS_MIN_COV     minimum coverage of `ivar variants` (default: 10)
IVAR_CONSENSUS_MIN_FREQ   minimum frequency of `ivar consensus` (default: 0.5)
IVAR_CONSENSUS_MIN_QUAL   minimum quality of `ivar consensus` (default: 20)
IVAR_CONSENSUS_MIN_COV    minimum coverage of `ivar consensus` (default: 50)

For Linux users only: you may need to add sudo in front of the poliopoly command since Docker by default requires sudo privileges. If you wish to not add sudo, you can instead add the user who runs the poliopoly command to user group docker:

sudo usermod -aG docker $USER

Replace "$USER" to other user name if it's not the user who runs the usermod command. The user need to logout and login again for activating the new group.

Troubleshooting

Memory requirement

The script requires at least 8GB minimum of free memory that dedicated for Docker.

For Linux users, since the Docker runs as a native program, the limit is the total free memory of the system:

free -h

For MacOS/Windows users, Docker runs in a virtual machine with allocated amount of memory. For both systems the default memory is 2GB which is insufficient. Follow the corresponding instruction for increasing the RAM/Memory:

• MacOS
• Windows

Disk space requirement

At least 30GB free disk space is required for running poliopoly. For Linux user this is the free space of where /var/lib/docker located:

df -h

For MacOS/Windows users, please follow the same instruction for memory to increase the "disk image size".

Clean up cache

You may want to clean up the cache files if you found poliopoly takes too much disk space or not functional properly. To do so, just run a single command:

docker volume rm poliopoly-work