rocpengliu/satanalyzer repository overview

SatAnalyzer: towards comprehensive microsatellite genotyping and visualization from sequencing data.
SatAnalyzer is a user-friendly, website-based platform developed in HTML, Java, JavaScript and R. It calls the genotyping software Seq2Sat⁠ under the license GUN GPL⁠, which is an standalone software developed in C++.
SatAnalyzer allows users to manually edit/correct the genotype generated by auto-scoring in Seq2Sat.
SatAnalyzer also conducts reads quality check and visualize reads quality.

STEPS:

1. Download (https://www.docker.com/products/docker-desktop/⁠) and install docker in your local computer

2. Run SatAnalyzer in docker

   2.1 for Linux

      2.1.1. open a terminal
   
      2.1.2. sudo docker pull rocpengliu/satanalyzer:latest
   
      2.1.3. sudo docker run -ti --rm -p 8080:8080 -v /:/data rocpengliu/satanalyzer:latest
   

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   2.2 for Windows

      2.2.1. open a terminal from "Power Shell" (not from  "Command Prompt")
   
      2.2.2. docker pull rocpengliu/satanalyzer:latest
   
      2.2.3. if your working directory (your data folder) is at C:\ drive, run the following command (change C:\ to D:\ if your data is in D:\ drive):
              docker run -ti --rm -p 8080:8080 -v C:\:/data rocpengliu/satanalyzer:latest
   

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3. Click http://localhost:8080/SatAnalyzer⁠ to launch SatAnalyzer

4. From the website interface, click "TUTORIALS" for how to analyze your data using SatAnalyzer

Tutorial

1. Please click here⁠ for a tutorial in pdf on installing SatAnalyzer in docker and analyzing data in SatAnalyzer..
2. Please click here⁠ for a video tutorial on installing SatAnalyzer in docker and analyzing data in SatAnalyzer.

Example Data

You can download small example data from Seq2Sat⁠.

Support

If you have any questions, please contact [email protected]⁠

License

SatAnalyzer is available under the terms of the GNU GPL 2⁠.

Please cite

Liu, P., Wilson, P., Redquest, B., Keobouasone, S., & Manseau, M. (2024). Seq2Sat and SatAnalyzer toolkit: towards comprehensive microsatellite genotyping from sequencing data. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13929⁠