Xue, H.; Gallopin, M.; Marchet, C.; Nguyen, T. N. H.; Wang, Y.; Bessiere, C.; Gautheret, D.

KaMRaT is a program for processing large k-mer count tables extracted from high throughput sequencing data. Major functions include scoring k-mers based on count statistics, merging overlapping k-mers into longer contigs and selecting k-mers based on their presence in certain samples. KaMRaT\'s main application is the reference-free analysis of multi-sample and multi-condition datasets from RNA-seq, as well as ChiP-seq or ribo-seq experiments. KaMRaT enables the identification of condition-specific or differential sequences, irrespective of any gene or transcript annotation. Implementation and availability: KaMRaT is implemented in C++. Source code and documentation are available via https:// github.com/Transipedia/KaMRaT. Container images are available via https://hub.docker. com/r/xuehl/kamrat.