npScarf

npScarf performs real-time hybrid scaffolding by integrating nanopore long reads with short-read assemblies to complete fragmented genomes and resolve repeats.

Key Features:

• Real-Time Scaffolding and Completion: Scaffolds and completes fragmented short-read assemblies by incorporating streaming nanopore long reads during the sequencing run.
• Continuous Quality Reporting: Reports assembly metrics in real time to monitor assembly quality and completeness as sequencing proceeds.
• Efficiency in Data Usage: Reduces required sequencing data by using long reads to close gaps and improve assembly completeness with fewer reads than short-read-only approaches.
• Resource Optimization: Requires reduced computational resources compared with traditional assembly workflows.

Scientific Applications:

• Complex repeat resolution: Spans and resolves complex repeat regions that are ambiguous in short-read assemblies using long reads.
• Bacterial and eukaryotic genome assembly: Applies hybrid scaffolding to produce more complete assemblies for bacterial and eukaryotic genomes.

Methodology:

Integrates streaming nanopore long reads with existing short-read assemblies to perform hybrid scaffolding in real time, spanning repeats and resolving assembly ambiguities.