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

ABSTRACT:

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.

SUBMITTER: Xue H 

PROVIDER: S-EPMC10942800 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature