VirusDetect is a software package that can efficiently and exhaustively analyze large-scale sRNA datasets for virus identification. The program performs reference-guided assembly by aligning sRNA reads to the known virus reference database (GenBank gbvrl) as well as de novo assembly using Velvet with automated parameter optimization. The assembled contigs are compared to the reference virus sequences for virus identification. The contigs were treated as undetermined contigs if they are not hit to any known viruses. The siRNA profile of these undetermined contigs are provided as guidance to discovery novel viruses which do not show sequence similarity with known viruses.