MSP is implemented in Java and thus can run on both Linux and Windows platforms.

MSPGraphBuilder

MSPGraphBuilder is a de Bruijn graph constructor based on the minimum substring partitioning technique. It can significantly reduce the memory consumption in building de Bruijn graph while without runtime slowdown. MSPGraphBuilder is a command-line program that reads DNA sequences in FASTA format and outputs the de Bruijn graph in either binary or readable text format. Please refer to the manual below for more details.

Download MSPGraphBuilder

Latest stable release (0.10.0):
MSPGraphBuilder-0.10.0.zip executable package
MSPGraphBuilder-0.10.0-src.zip source code
manual-MSPGraphBuilder-0.10.0.pdf manual

MSPKmerCounter

MSPKmerCounter is a k-mer counter based on the minimum substring partitioning technique. It can count the appearances of k-mers in a fast and memory-efficient manner. MSPCounter is a command-line program that reads DNA sequences in FASTA format. It outputs the k-mer counts in binary format, which can be converted into the readable text format using the "Dump" command. Please refer to the manual below for more details.

Download MSPKmerCounter

Latest stable release (0.10.0):
MSPKmerCounter-0.10.0.zip executable package
MSPKmerCounter-0.10.0-src.zip source code
manual-MSPKmerCounter-0.10.0.pdf manual

Usage agreement

Downloading is for internal research purpose only. Redistribution and commercial usage are not permitted. For other interests, contact the authors.