LoopViz

LoopViz analyzes long-read Oxford Nanopore Technologies (ONT) sequencing data to identify and validate full-length plasmid sequences from uLOOP assembly reactions.

Key Features:

• Quality control and visualization: Quantifies and visualizes assembly reaction results to identify full-length reads originating from individual plasmids within a population.
• Full-length read identification: Detects reads that span entire plasmid constructs to determine complete plasmid sequences.
• Alignment to user-provided fragment files: Aligns reads to user-provided DNA fragment files to determine plasmid composition and fragment arrangement.
• Comprehensive QC statistics: Generates detailed quality control statistics for cloning and ONT sequencing reactions.
• Resolution of repetitive/meta-regions: Resolves repetitive meta-regions and other complex sequence features that are challenging for short-read assembly.
• Long-read sequencing integration: Leverages Oxford Nanopore Technologies (ONT) long-read sequencing to determine plasmid sequences from complex libraries.

Scientific Applications:

• uLOOP assembly validation: Validates and characterizes products of uLOOP recursive, Golden Gate-like assembly reactions.
• Plasmid population analysis: Characterizes complex plasmid populations generated in single-reaction libraries to identify variant constructs.
• Transcriptional unit (TU) library characterization: Determines composition and arrangement of transcriptional unit (TU) libraries within plasmids.
• Refactoring and pathway verification: Supports exploration, refactoring, and verification of novel genetic pathways by providing complete plasmid sequence information.

Methodology:

Analyzes ONT long-read sequencing data, identifies full-length plasmid reads, aligns those reads to user-provided DNA fragment files, and computes quality control statistics used for visualization of assembly results.