A software package that discovers, annotates, and genotypes non-reference mobile element insertions (MEIs) in Illumina DNA paired-end whole genome sequencing (WGS) data. MELT was first conceived as a tool to identify non-reference MEIs in large genome sequencing projects, specifically as part of the 1000 Genomes Project, and has been further optimized to run on a wide range of data types. MELT is optimized for performing discovery in a large number of individual sequencing samples using the sun grid engine (SGE). MELT also has two additional workflows: analysis without SGE (for adaptability to other parallel computing platforms) and single genome analysis. MELT is highly scalable for many different types of data.