We have validated our method on simulated error-free reads, FlowSim-simulated reads with sequencing errors, and real 454 pyrosequencing reads from HCV and HIV samples. We are currently exploring extensions of ViSpA to paired-end reads; the main difficulty is selection of pair-aware candidate paths. We also foresee application of ViSpA's techniques to the analysis of high-throughput sequencing data from microbial communities [23] and ecological samples of eukaryote populations [35] .