github.com/dib-lab/kProcessor ↗
kProcessor: kmers processing framework.
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2018-05-29
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2020-07-27
About dib-lab/kProcessor
kProcessor is a C++ framework for processing kmers, the short DNA or RNA sequences used in genomic analysis, with a convenient Python interface. The core of the system revolves around two virtual data structures: kDataFrame stores kmers along with associated metadata like counts and custom columns, while Colored kDataFrame extends this to index kmers across multiple reference sequences by mapping them to color keys rather than counts.
The library enables users to manipulate kmer data efficiently through various operations including merging multiple kDataFrames and applying set operations like union, intersection, and difference. It's designed to handle both simple count-based kmer analysis and more complex multi-sequence indexing scenarios. The project can be installed via pip for quick setup or built from source using CMake, with optional components for testing and documentation generation.
kProcessor is built and maintained by the DIB Lab and is distributed under the BSD-3-Clause license. Python bindings are generated using SWIG, allowing researchers and bioinformaticians to leverage the C++ performance while working in a more accessible Python environment.