miRTop

miRTop standardizes miRNA and isomiR small RNA-seq outputs using the mirGFF3 format to enable unified annotation and conversion for downstream analysis.

Key Features:

• mirGFF3 format: An extension of the GFF3 standard tailored for small RNA-seq data that unifies miRNA and isomiR annotations across tools.
• mirtop command-line tool: A Python-based CLI for creating, managing, and converting datasets into mirGFF3 files.
• Input conversion support: Conversion from outputs generated by seqbuster, isomiR-SEA, sRNAbench, Prost!, and from BAM files into mirGFF3.
• Integration with existing tools: mirGFF3 has been integrated into miRge2.0, IsoMIRmap, and OptimiR codebases.
• Open architecture: mirtop allows external tools and pipelines to emit or convert results to mirGFF3 to promote interoperability.

Scientific Applications:

• Standardized annotation: Provides a consistent format for annotating miRNAs and isomiRs across studies and tools.
• Data sharing and comparison: Enables comparison and sharing of miRNA/isomiR quantifications between pipelines and research groups.
• Downstream tool compatibility: Facilitates development of analysis tools that consume a common mirGFF3 representation.
• Reproducibility and accuracy: Supports reproducible miRNA-seq analyses by reducing format-related discrepancies.

Methodology:

Creation, management, and conversion of mirGFF3 files using the mirtop Python command-line tool, including conversion from seqbuster, isomiR-SEA, sRNAbench, Prost!, and BAM file outputs; mirGFF3 is specified as an extension of GFF3 for small RNA-seq data.