Source code of the TRITEX pipeline for chromosome-scale assembly of Triticeae genomes. The most recent source code version is accessible from a public Bitbucket repository (https://bitbucket.org/tritexassembly/tritexassembly.bitbucket.io). This DOI holds the source code as of September 16th 2019 (commit: 7041ff2). A detailed usage guide can be found here: https://tritexassembly.bitbucket.io. The pipeline is described in the preprint Monat al. (2019) BioRxiv, https://doi.org/10.1101/631648.