STRipy's documentation

Installation instructions

Please select your operating system for installation and set-up instructions.

Easy way (by using compiled binaries)

It is very easy to run STRipy by using the pre-compiled binaries. Download the compressed file and unpack the file (double-click on file). Drag STRipy.app to the Applications folder. Open STRipy from the Applications folder.

NB! When running the application for the first time you will get a security warning saying this app cannot be opened because the developer cannot be verified. Click "Cancel" to close the window and then go to "System Preferences", click on "Security & Privacy" and under the "General" tab (at the bottom) it should say: "STRipy was blocked from use because it is not from an identified developer". Click "Open Anyway" and also "Open" on the pop-up window.

If instead of STRipy there is a name of another application, then you need to make a choice for this one to remove the notification and display the one related to STRipy.

Run from source

You can also run the application from the source code. In order to do that, first make sure you have Python 3.8+ in your system. Then download STRipy from git repository git clone https://gitlab.com/andreassh/stripy-client.git and go to the downloaded folder cd stripy-client/

Install all required packages by executing: python3 -m pip install -r requirements.txt. In additional, you might also need to run: python3 -m pip install pywebview[qt]

When all required packages are installed, you can run the application through terminal by simply executing: python3 stri.py

Compile from source code

To create the application for macOS from source, firstly install py2app library for Python: python3 -m pip install py2app and then in the stripy-client folder run python3 create-macOS-app.py py2app (STRipy.app will be saved into the "dist" folder, which then needs to be dragged to the Applications folder).

Easy way (by using compiled binaries)

It is very easy to run STRipy by using the pre-compiled binaries. Download the compressed file. Unpack the file and then open Terminal, go to that folder and run STRipy by executing: ./STRipy

If you want to do everything through command line, then please run the following commands:
wget https://stripy.org/download/STRipy-v1.1-Linux.tar.gz
tar -xzvf STRipy-v1.1-Linux.tar.gz
./STRipy

Run from source

You can also run the application from the source code. In order to do that, first make sure you have Python 3.8+ in your system. Then download STRipy from git repository:
git clone https://gitlab.com/andreassh/stripy-client.git and go to the downloaded folder: cd stripy-client/

Install all required packages by executing: python3 -m pip install -r requirements.txt. In additional, you might also need to run: python3 -m pip install pywebview[qt]

When all required packages are installed, you can run the application through terminal by simply executing: python3 stri.py

Compile from source code

To create the executable file that is suitable for using in Linux, firstly install py2installer library for Python: python3 -m pip install pyinstaller and then in the stripy-client folder run: pyinstaller stri.py --name STRipy --onefile --hidden-import pysam.libctabixproxies --add-data "assets:assets" --icon icon.icns --upx-dir=..\upx391w (The executable file will be saved into the "dist" folder).

Easy way (by using compiled binaries)

It is also possible to run the Linux version of STRipy in Windows 10/11 through WSL.

To do that, there are few steps that has to be taken (only once). First of all, set up WSL in Windows 10/11 and install a Linux distribution (such as Ubuntu): https://docs.microsoft.com/en-us/windows/wsl/install

Please note that the installed Linux is a minimal OS without a graphical interface and it is missing the libraries required to run STRipy. Therefore, in order to successfully run STRipy, you need to download and install Xming X Server for Windows from https://sourceforge.net/projects/xming which will enable launching graphical applications.

Next, when you have opened the installed Linux distribution (a new window has opened where you can enter commands), you need to enable Web content engine library for GTK. To install and enable this, please run:
sudo apt update
sudo apt install girl1.2-webkit2-4.0
export DISPLAY=:0

Finally, download STRipy, unpack and run:
wget https://stripy.org/download/STRipy-v1.1-Linux.tar.gz
tar -xzvf STRipy-v1.1-Linux.tar.gz
./STRipy

Next time when you want to run STRipy, you only need to execute the last command (./STRipy) in the folder containing STRipy's application.

Run from source

You can also run the application from the source code. In order to do that, first make sure you have Python 3.8+ in your system. Then download STRipy from git repository:
git clone https://gitlab.com/andreassh/stripy-client.git and go to the downloaded folder: cd stripy-client/

Install all required packages by executing: python3 -m pip install -r requirements.txt. In additional, you might also need to run: python3 -m pip install pywebview[qt]

When all required packages are installed, you can run the application through terminal by simply executing: python3 stri.py

Compile from source code

To create the executable file that is suitable for using in Linux, firstly install py2installer library for Python: python3 -m pip install pyinstaller and then in the stripy-client folder run: pyinstaller stri.py --name STRipy --onefile --hidden-import pysam.libctabixproxies --add-data "assets:assets" --icon icon.icns --upx-dir=..\upx391w (The executable file will be saved into the "dist" folder).


Using the application

Genotyping a sample

It is very easy to use STRipy. To genotype a sample, please select the following on the home screen:

  1. Select from drop-down list either a Disease or Locus to target
  2. Choose the aligned and indexed BAM or CRAM file of the Sample you want to genotype
  3. If the selected locus is in one of the sex chromosomes, then select the selected sample's Sex (or let STRipy to detect this automatically, but always double-check the result)
  4. Select the name of the Genome assembly which was used to align the selected BAM or CRAM file (or let STRipy to detect this automatically)
  5. Choose the type of Analysis which can be either Standard or Extended:
    • Standard: fast analysis (often between 5-15 seconds) which is recommended to use at the first try. Maximum detectable repeat size is limited to the fragment length.
    • Extended: slower analysis (usually between 20 seconds to few minutes) which can be used when you want to expand the genotyping ability past the fragment length. This could be good to try when STRipy notifies of a potentially long allele or when you suspect an allele that is at least ~few hundred bp long. NB! Analysis of long STR alleles from short-read sequencing data is very complicated and often results either a under- or overestimated allele. Use this option carefully.
  6. Pick a Server where the genotyping takes place. Unless you have set up your own server, then Cloud is the only activated option.

Viewing results

The following colour scheme is used which is based on data acquired from the literature:

Green
- determined length of an allele is in the normal range;
Orange
- determined length of an allele is in the intermediate range;
Red
- determined length of an allele is in the pathogenic range;
Grey
- determined length of an allele is none of the above ranges and therefore considered to be as in the "unknown" range.

Pink dot in the "Genotype" section is used to mark an allele that is a population outlier (Z-score ≥3.718). Population data is acquired by genotyping 1000 Genomes Project cohort.

Results in the "Genotype" section as well as the first row of the "Extra" section are coming from ExpansionHunter.

Bottom row in the "Extra" section displays results that are determined by STRipy. STRipy is analysing all reads and only counting the exact pathogenic repeat units (without substitutions/interruptions) in spanning and flanking reads, which is then reported with the number of reads in parentheses. Additionally, STRipy reports the number of reads that are fully made of the pathogenic repeat unit that can indicate a long allele. The bottom row is important while analysing replaced or nested type of repeats because ExpansionHunter counts the non-pathogenic repeat unit as well and as a result, reports a genotype which may not contain the pathogenic motif at all.

Read alignments/pileups for the STR locus can be viewed under the Alignment visualiser tab. This is a output of REViewer which then is colourised by STRipy based on the aforementioned colour scheme. Read alignments can be saved as a PDF file by clicking on the button.

Genotyping results can be saved as a PDF file by clicking on the button.