HipMer is the first end-to-end de novo genome assembler designed for extreme scale analysis via efficient parallelization. The single-genome assembly implementation is a high-performance parallelization and port of the Meraculous assembler (http://jgi.doe.gov/data-and-tools/meraculous/). The metaHipMer extension is a recent addition to HipMer that is geared to large metagenomes and leverages iterative kmer sizes and a specialized scaffolding algorithm to produce increased contiguity and accuracy in metagenomic assemblies. It is able to reconstruct rRNA elements via a separate algorithm which relies on reference SSU and LSU Hidden Markov Models to help traverse the contig graph around ribosomal RNA regions.
This work has recently been extended in HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks. https://academic.oup.com/nar/article/46/6/e33/4791133