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bioRxiv · 10.1101/2024.01.15.575511

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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Abstract

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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Xue, H., Gallopin, M., Marchet, C., Nguyen, T. N. H., Wang, Y., Bessiere, C., Gautheret, D.. 2024-01-16. KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction. https://doi.org/10.1101/2024.01.15.575511

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