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Published on: October 11, 2018
KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction
Haoliang Xue1, Mélina Gallopin1, Camille Marchet2
1I2BC, Université Paris-Saclay, CNRS, CEA, 91190 Gif-sur-Yvette, France.
Motivation:
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.
Results:
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.
Availability And Implementation:
Source code and documentation are available via https://github.com/Transipedia/KaMRaT.
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