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Daniel Gómez-Sánchez edited this page Feb 7, 2017 · 21 revisions

ReadTools: Standardizing Sources For Sequencing Data

ReadTools provides a consistent and highly tested set of tools for processing any kind of source of sequencing data, focusing in raw reads (although it also include tools for mapped reads).

Diverse formats were develop for store 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 different sources for sequencing data.

Download

Executable jar files for all and released versions could be found under [Releases]. For using unreleased versions, 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 long 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

[SAM specs]: http://samtools.github.io/hts-specs/ [Read sources]: https://github.com/magicDGS/ReadTools/wiki/Read-sources [Releases]: https://github.com/magicDGS/ReadTools/releases [README]: https://github.com/magicDGS/ReadTools/blob/dgs_update_readme/README.md [CHANGELOG]: https://github.com/magicDGS/ReadTools/blob/dgs_update_readme/CHANGELOG.md

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