KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction
Xue, H.; Gallopin, M.; Marchet, C.; Nguyen, T. N. H.; Wang, Y.; Bessiere, C.; Gautheret, D.
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SummaryKaMRaT 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 availabilityKaMRaT 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.
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