s-aligner: a greedy algorithm for non-greedy de novo genome assembly

Genome assembly is a fundamental tool for biological research. Particularly, in microbiology, where budgets per sample are often scarce, it can make the difference between an inconclusive result and a fully valid conclusion. Identifying new strains or estimating the relative abundance of quasi-species in a sample are some example tasks that cant be properly accomplished without previously generating assemblies with little structure ambiguity and covering most of the genome. In this work, we present a new genome assembly tool based on a greedy strategy. We compare the results obtained applying this tool to the results obtained with previously existing software. We find that, when applied to viral studies, comparatively, the software we developed often gets far larger contigs and higher genome fraction coverage than previous software. We also find a significant advantage when applied to exceptionally large virus genomes.