Small noncoding RNAs (sncRNAs) are widely expressed in the cell of almost all known species. Most sncRNAs appear to have regulatory roles, ranging from facilitating RNA production and modifications (e.g., snoRNAs) to control of mRNA stability and translational efficiency (e.g., miRNAs and endo-siRNA) and to transposon silencing (e.g., piRNAs). The affordability and efficiency of next-generation RNA deep sequencing (RNA-Seq) technologies have made sncRNA deep sequencing (sncRNA-Seq) analyses a routine in biomedical research. SncRNA-Seq analyses generate millions of reads and gigabytes of data; annotation of sncRNA-Seq data remains challenging due to a lack of comprehensive sncRNA annotation pipelines. To solve this problem, researchers at the University of Nevada School of Medicine have developed a computer-assisted sncRNA annotation pipeline, which uses open-source software and allows for not only proper classification of known sncRNAs, but also discovery of novel sncRNA species.