The QSR problem is related to several well-studied problems: de novo genome assembly [17] [18] [19] , haplotype assembly [20, 21] , population phasing [22] and metagenomics [23] . As noted above, de novo assembly methods are designed to reconstruct a single genome sequence, and are not well-suited for reconstructing a large number of closely related quasispecies sequences. Haplotype assembly does seek to reconstruct two closely related haplotype sequences, but existing methods do not easily extend to the reconstruction of a large (and a priori unknown) number of sequences. Computational methods developed for population phasing deal with large numbers of haplotypes, but rely on the availability of genotype data that conflates information about pairs of haplotypes. Metagenomic samples do consist of sequencing reads generated from the genomes of a large number of species. However, differences between the genomes of these species are considerably larger than those between viral quasispecies. Furthermore, existing tools for metagenomic data analysis focus on species identification, as reconstruction of complete genomic sequences would require much higher sequencing depth than that typically provided by current metagenomic datasets.