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.
Both released and unreleased changes are reported in the CHANGELOG.
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 --versionor
java -jar ReadTools.jar -v
License and citing
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