SAVAGE is a computational tool for reconstructing individual haplotypes of intra-host virus strains (a viral quasispecies) without the need for a high quality reference genome. SAVAGE makes use of either FM-index based data structures or ad-hoc consensus reference sequence for constructing overlap graphs from patient sample data. In this overlap graph, nodes represent reads and/or contigs, while edges reflect that two reads/contigs, based on sound statistical considerations, represent identical haplotypic sequence. Following an iterative scheme, a new overlap assembly algorithm that is based on the enumeration of statistically well-calibrated groups of reads/contigs then efficiently reconstructs the individual haplotypes from this overlap graph.

Evolutionary Intelligence

Baaijens, J., & Schönhuth, A. (2016). SAVAGE.