A variant caller and small genome assembler. The heart of DISCOVAR is a de novo genome assembler, one that is accurate enough to produce assemblies that can be used for variant calling given a reference sequence. DISCOVAR can also generate de novo assemblies for small genomes, but consider using DISCOVAR de novo instead which can assemble genomes up to mammalian size. DISCOVAR provides a more complete inventory of an individual’s genetic variants than had been previously possible. As such, it adds to the tools that can be used to probe the genetic basis of disease. It may be particularly useful in cases where targeted or exome sequencing fails to find causal mutations.