Viral Reads Assembly Enhancer (VIRAE) is a context-based trimming bioinformatics tool, especially designed for viral metagenomics, which allows Next Generation Sequencing (NGS) read decontamination based on any given reference sequence(s). VIRAE is powered by an updated version of Zero-Waste Algorithm (ZWA) and incorporates ready-to-use well-established bioinformatics software to detect and dissect partially mapped reads (chimeric reads) by specifically removing the moieties, which align to the given reference sequence(s). The clean output reads enhance de novo assembly performance, increasing the availability of reads for more accurate and more efficacious de novo virus genome assembly.