# KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction

## TL;DR

KaMRaT is a C++ toolkit for analyzing RNA-seq data to find sequences that are specific to certain conditions or differentially expressed.

## Contribution

KaMRaT introduces a new method for k-mer count matrix reduction in RNA-seq data without relying on gene annotations.

## Key findings

- KaMRaT identifies differentially expressed sequences using k-mer count statistics.
- The toolkit merges overlapping k-mers into contigs for improved analysis.
- It enables sample-specific k-mer selection based on occurrence patterns.

## Abstract

KaMRaT is designed for processing large k-mer count tables derived from multi-sample, RNA-seq data. Its primary objective is to identify condition-specific or differentially expressed sequences, regardless of gene or transcript annotation.

KaMRaT is implemented in C++. Major functions include scoring k-mers based on count statistics, merging overlapping k-mers into contigs and selecting k-mers based on their occurrence across specific samples.

Source code and documentation are available via https://github.com/Transipedia/KaMRaT.