miRge 2.0: An updated tool to comprehensively analyze microRNA sequencing data

miRNAs play important roles in the regulation of gene expression. The rapidly developing field of microRNA sequencing (miRNA-seq; small RNA-seq) needs comprehensive bioinformatics tools to analyze these large datasets. We present the second iteration of miRge, miRge 2.0, with multiple enhancements. miRge 2.0 adds new functionality including novel miRNA detection, A-to-I editing analysis, better output files, and improved alignment to miRNAs. Our novel miRNA detection method is the first to use both miRNA hairpin sequence structure and composition of isomiRs resulting in a more specific capture of potential miRNAs. Using known miRNA data, our support vector machine (SVM) model predicted miRNAs with an average Matthews correlation coefficient (MCC) of 0.939 over 32 human cell datasets and outperformed miRDeep2 and miRAnalyzer regarding phylogenetic conservation. The A-to-I editing analysis implementation strongly correlated with a reference datasets prior analysis with adjusted R2 = 0.96. miRge 2.0 comes with alignment libraries to both miRBase v21 and MirGeneDB for 6 species: human, mouse, rat, fruit fly, nematode and zebrafish; and has a tool to create custom libraries. With the redevelopment of the tool in Python, it is now incorporated into bcbio-nextgen and implementable through Bioconda. miRge 2.0 is freely available at: https://github.com/mhalushka/miRge.