miRge3

miRge3 processes next-generation small RNA sequencing (NGS) data to annotate and quantify microRNAs (miRNAs) and tRNA-derived fragments (tRFs) and to predict novel miRNAs for small non-coding RNA research.

Key Features:

• Alignment pipeline: Robust alignment pipelines for annotation and analysis of small non-coding RNAs from NGS datasets.
• Cutadapt and Python compatibility: Compatible with newer versions of Cutadapt and Python to integrate with preprocessing and analysis workflows.
• Unique Molecular Identifier (UMI) processing: UMI handling to account for PCR duplicates during miRNA quantification.
• IsomiR analysis (GFF3): Accurate isomiR analysis with GFF3-formatted output for sequence variant annotation within miRNA populations.
• Speed and efficiency: Benchmarking reports improved runtime performance relative to miRge2.0, Chimira, and sRNAbench.
• Novel miRNA prediction: Prediction of novel miRNAs using a support vector machine (SVM) approach.
• Integration with bioinformatics packages: Output formats and analyses designed for integration with other bioinformatics tools and pipelines.
• Library preparation support: Support for building small-RNA libraries tailored to specific organisms for use with the pipeline.

Scientific Applications:

• miRNA and tRF quantification: Quantitative analysis of miRNAs and tRNA-derived fragments from small RNA-seq experiments.
• IsomiR characterization: Detailed annotation and analysis of miRNA sequence variants (isomiRs) using GFF3 output.
• Novel small RNA discovery: Identification of candidate novel miRNAs via machine-learning prediction.
• Study of RNA-mediated regulation: Investigation of translational regulation and gene expression modulation mediated by small non-coding RNAs.
• Analysis of RNA editing and processing: Examination of RNA editing events and processing-derived fragments in small RNA populations.
• Integration in multi-step analyses: Use as a component in complex bioinformatics workflows through interoperable outputs.

Methodology:

Computational methods explicitly include alignment pipelines for small RNA annotation from NGS data, compatibility with Cutadapt and Python, UMI processing to collapse PCR duplicates, GFF3-formatted isomiR analysis, and novel miRNA prediction using a support vector machine.