MasterOfPores

MasterOfPores processes Oxford Nanopore Technologies direct RNA sequencing data to convert raw current signals into base-called, mapped, and quantified outputs for RNA modification detection, poly(A) tail length estimation, and isoform-level analyses.

Key Features:

• Direct RNA sequencing capability: Supports Oxford Nanopore direct RNA sequencing to analyze native RNA molecules without cDNA conversion.
• Raw signal processing: Converts raw nanopore current intensities into processed data and quality metrics.
• Quality assessment and filtering: Implements quality assessment and filtering of reads and signal-derived data.
• Base-calling: Performs base-calling of nanopore signal into nucleotide sequences.
• Mapping: Maps reads to reference genomes or transcripts for downstream analyses.
• Quantification and outputs: Produces per-gene counts, RNA modification profiles, poly(A) tail length predictions, and RNA isoform identifications.
• Nextflow integration: Implemented in Nextflow to enable parallelization and portability across computing environments.
• Containerization: Uses Docker and Singularity containers to ensure reproducible execution.

Scientific Applications:

• Epitranscriptomics: Detection and profiling of RNA modifications from nanopore signal to study chemical modifications on RNA.
• Poly(A) tail analysis: Single-molecule estimation of poly(A) tail lengths to investigate RNA stability and dynamics.
• Isoform-level transcriptomics: Identification of RNA isoforms from long reads to characterize transcript diversity.
• Gene expression quantification: Generation of per-gene counts from mapped reads for differential expression and transcriptomic studies.

Methodology:

Conversion of raw nanopore current intensities into processed data, followed by quality assessment and filtering, base-calling, and mapping to reference genomes or transcripts within a modular Nextflow workflow executed using Docker or Singularity containers.