ReadTools is an open‐source toolkit designed to standardize and pre-process sequencing read data from different platforms. It manages FASTQ‐ and SAM‐formatted inputs while dealing with platform‐specific peculiarities and provides a standard SAM compliant output.
For more user-friendly information about the project, visit our Documentation Page. There, you can find the information for download and the complete tool documentation for the current version.
- A Java 8 JDK
- Git 2.5 or greater
- Gradle 4.8 or greater
Important: to build ReadTools, you should clone the git repository (release zip files would not work).
git clone https://github.com/magicDGS/ReadTools.git
cd ReadTools
./gradlew currentJar
The jar file would be located in build/libs/ReadTools.jar.
To build a released version of ReadTools, use git checkout ${version_number}.
Please read CONTRIBUTING.md for details on our code of conduct, and the process for collaborating on the project.
For developers, please check our Wiki for more details. If you have any question uncovered by the Wiki, feel free to fill in an issue: we would be happy to include any extra information with your feedback!
Before submitting a new bug report, please search for keywords in our Issue Tracker. If you cannot find your problem, fill in a new issue.
This project adheres to Semantic Versioning (SemVer) for the user-side. A short description with notable changes appears in each release. All the changes can be found in the CHANGELOG.
ReadTools is licensed under the MIT License. See LICENSE file.
If you use ReadTools, please cite:
Gómez-Sánchez D, Schlötterer C. ReadTools: A universal toolkit for handling sequence data from different sequencing platforms. Mol Ecol Resour. 2017;00:1–5. doi:10.1111/1755-0998.12741