HipMer Portal
HipMer is a high-performance application that produces high-quality de novo assemblies for very large-scale single genomes. It is maintained but no longer actively developed. For metagenomes, use MetaHipMer.
HipMer Publications
HipMer and its components are described in detail in the following publications:
HipMer: An Extreme-Scale De Novo Genome Assembler. E. Georganas et al, SC 2015merAligner: A Fully Parallel Sequence Aligner. E. Georganas et al, IPDPS 2015
Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly. E. Georganas et al, SC 2014
HipMer Source Code
The source code for HipMer is available under an open-source MIT license and can be downloaded from