A universal toolkit for handling sequence data from different sequencing platforms

ReadTools provides a consistent and highly tested set of tools for processing sequencing data from any kind of source and focusing on raw reads, while including tools for mapped reads as well.

Diverse formats were developed for storing reads (see Read sources), but ReadTools opt for following the SAM specs to maintain a common data format to store both raw/mapped reads. Thus, ReadTools also helps to standardize sequencing data in different formats.

Download

Github Releases

Download the latest executable jar from the top of the page. Previous versions can be retrieved from the GitHub Releases page. If you would like to use an unreleased version, see the README.

Both released and unreleased changes are reported in the CHANGELOG.

Main usage

To obtain a list of implemented tools run the following command:

java -jar ReadTools.jar

For a detailed description of each tool:

java -jar ReadTools.jar <toolName> --help

For getting the packaged version:

java -jar ReadTools.jar --version or java -jar ReadTools.jar -v

Bug reports

Please, if you find any problem use our issue tracker or contact by email daniel.gomez.sanchez@hotmail.es

License and citing

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