miRge

miRge is a logical, ultrafast, small RNA-seq solution to process samples in a highly multiplexed fashion, resulting in dramatically decreased computational requirements when processing sets of samples in a single run. It utilizes a unique sequential alignment algorithm for annotation of small RNA-seq data. Output is given for miRNAs as raw reads and reads per million (RPM) in addition to isomiR data and reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA). IsomiR entropy can be determined for each sample or across samples in a multiplex run.