KaMRaT: a C++ toolkit fork-mer count matrix dimension reduction

Abstract

AbstractSummaryKaMRaTis a program for processing largek-mer count tables extracted from high throughput sequencing data. Major functions include scoringk-mers based on count statistics, merging overlappingk-mers into longer contigs and selectingk-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.KaMRaTenables the identification of condition-specific or differential sequences, irrespective of any gene or transcript annotation.Implementation and availabilityKaMRaTis implemented in C++. Source code and documentation are available viahttps://github.com/Transipedia/KaMRaT. Container images are available viahttps://hub.docker.com/r/xuehl/kamrat.