MiRspring

MiRspring generates compact HTML/JavaScript "miRspring" documents that reproduce and visualize miRNA sequencing data from BAM files to profile miRNA processing variants and identify isomiRs.

Key Features:

• miRspring document generation: Generates a compact HTML/JavaScript "miRspring document" that reproduces miRNA sequencing data from BAM files.
• Index-compression algorithm: Implements an index-compression algorithm to compress complete miRNA sequence datasets into a small document while preserving full sequence information.
• Visualization and analysis: Provides embedded visualization and analysis of miRNA sequences and processing variants within the miRspring document.
• Quality assessment: Assesses quality parameters of miRNA sequencing datasets.
• miRNA cluster expression: Evaluates miRNA cluster expression levels.
• Seed-isomiR discovery: Identifies and reports seed-isomiRs, noting that approximately 30% of human miRBase entries may have seed-isomiRs.
• Dataset-scale analysis: Applied to the analysis of 73 public datasets.

Scientific Applications:

• miRNA sequence profiling and variant analysis: Enables profiling of miRNA processing variants and isomiRs from sequencing data.
• Quality control of miRNA-seq data: Supports assessment of sequencing quality parameters for miRNA datasets.
• miRNA cluster expression analysis: Allows evaluation of expression levels within miRNA clusters.
• Discovery and characterization of seed-isomiRs: Facilitates identification and reporting of seed-isomiRs across datasets and miRBase entries.
• Reproducible encoding of sequence data: Encodes complete miRNA sequence information into a compact document format for reproducible analyses.

Methodology:

Generates miRspring HTML/JavaScript documents from BAM files using an index-compression algorithm, and analyses reported include processing of 73 public datasets.