Illustration of the principles of the PFOR2 and SLS computational programs.

(A) Flowchart showing the steps followed by PFOR2 for filtering all non-overlapping small RNAs (singleton) and terminal small RNAs (TSRs) with multi-thread processing and the assembly of the remaining true internal small RNAs (ISRs). (B) Schematic view of the virtual dicing of longer RNA reads into small overlapping sRNAs by SLS. (C) Close-up view of the filtering criterion of TSRs implemented in PFOR2. Each sRNA in the small fragments pool is placed into one of four groups based on the presence or absence of 5' and 3' overlapping sRNAs.