biotechvana/npstat repository overview

⁠npstat

Population genetics tests and estimators for pooled NGS data that can be applied to pooled sequences from Next Generation Sequencing experiments. The statistics are described in the paper "Population genomics from pool sequencing" by L. Ferretti, S.E. Ramos-Onsins and M. Perez-Enciso, Molecular Ecology (2013), DOI: 10.1111/mec.12522.

Image for https://github.com/lucaferretti/npstat⁠

⁠Using NPStat container

Before using the container, you need to pull the image from Docker Hub. The image is available at the following location: biotechvana/npstat⁠.

⁠Pull the image from docker hub

docker pull biotechvana/npstat

tag the image, if you want to use a different name or to avoid using the long image name

docker tag biotechvana/npstat npstat

Verify that the image has been successfully pulled by running the following command:

docker run --rm npstat

⁠Using the Docker Container

To run the NPStat application, use the following command:

docker run --rm npstat

This command will display the usage information for NPStat.

⁠Running NPStat with Data:

To analyze specific data, you can mount a local directory containing your data files to the container and specify the input files. For example:

docker run --rm -v /path/to/data:/data npstat  -n sample_size -l window_length [options] FILE.pileup

• Replace sample_size with the haploid sample size.
• Replace window_length with the window length in bases.
• Replace /path/to/data with the path to your local directory containing the data files and input_file with the name of your input file.
• Note: that :/data specifies the mount point inside the container where the data files will be available and mounted as the current working directory. And the mount point /data is fixed inside the container and should not be changed. /data is also the default working directory inside the container.

For example, if you have a data file named FILE.pileup in a directory /home/user/npstat_data, you can run NPStat as follows:

docker run --rm -v /home/user/npstat_data:/data npstat -i /data/FILE.pileup

## as /data is the working directory inside the container, you can also run it as follows
docker run --rm -v /home/user/npstat_data:/data npstat -i FILE.pileup

another example if you have a data file named FILE.pileup in your current directory, you can run NPStat as follows:

docker run --rm -v $(pwd):/data npstat -i FILE.pileup
## or
docker run --rm -v ./:/data npstat -i FILE.pileup

Output: The output file will be generated in the same directory where the input file is located.