MoP2

MoP2 processes direct RNA sequencing data generated by Oxford Nanopore Technologies' MinION to enable transcriptomic and epitranscriptomic analyses.

Key Features:

• Workflow orchestration: Implements Nextflow DSL2 and Linux containers for reproducible, modular execution.
• Input processing (FAST5): Pre-processes raw FAST5 files from Nanopore sequencing as the initial workflow stage.
• Basecalling: Performs basecalling to convert raw electrical signals into nucleotide sequences.
• Read quality control: Executes read quality control and filtering to retain high-quality reads for downstream analysis.
• Demultiplexing: Performs demultiplexing to sort reads by sample.
• GPU acceleration: Utilizes GPU computing during basecalling and demultiplexing to increase computational efficiency.
• Mapping: Maps reads to reference genomes or transcriptomes for alignment-based analyses.
• Quantification: Estimates per-gene and per-transcript abundances for expression analysis.
• Transcriptome assembly: Assembles transcriptomes to identify transcripts and transcript structures.
• Poly(A) tail length estimation: Estimates RNA poly(A) tail lengths for post-transcriptional analysis.
• RNA modification detection: Identifies RNA modifications for epitranscriptomic profiling.

Scientific Applications:

• Transcriptomic analysis: Quantifies gene and transcript expression and supports transcriptome assembly from direct RNA sequencing.
• Epitranscriptomic profiling: Detects RNA modifications and estimates poly(A) tail lengths to study post-transcriptional regulation.
• Nanopore direct RNA sequencing datasets: Processes datasets generated on Oxford Nanopore Technologies' MinION platform.
• Saccharomyces cerevisiae example: Demonstrated workflow application on S. cerevisiae total RNA samples.

Methodology:

Implements Nextflow DSL2 with Linux containers and performs preprocessing of FAST5 files, basecalling, read quality control, demultiplexing and filtering (with optional GPU acceleration for basecalling and demultiplexing), mapping to reference genomes or transcriptomes, per-gene/transcript abundance estimation, transcriptome assembly, poly(A) tail length estimation, and RNA modification identification.