runBNG

runBNG integrates BioNano genomic analysis tools into a command-line pipeline to analyze optical mapping single-molecule maps, performing quality control, de novo assembly, comparative analysis, super-scaffolding, and structural variation detection.

Key Features:

• Quality Control: Implements robust quality control measures for optical mapping single-molecule maps to assess data reliability.
• De Novo Assembly: Supports optical map de novo assembly to construct genome maps without a reference sequence.
• Comparative Analysis: Enables detailed comparisons between optical maps to identify variations and similarities across datasets.
• Super-Scaffolding: Integrates contigs into larger scaffolds using optical mapping data to improve assembly contiguity and structural resolution.
• Structural Variation Detection: Detects large-scale structural variations within genomic data derived from optical maps.
• Integration of BioNano Tools: Encapsulates a suite of BioNano genomic analysis tools into a cohesive pipeline for single-script execution.
• Customizability: Provides options to tailor analysis steps and parameters within the integrated pipeline.

Scientific Applications:

• Genome assembly: Generation and improvement of genome assemblies using optical mapping data and de novo assembly methods.
• Structural variant analysis: Identification and characterization of large-scale genomic rearrangements from optical maps.
• Comparative genomics: Comparative analysis of optical maps across samples or assemblies to study genomic differences and similarities.

Methodology:

Operates as a single bash script on the command line that integrates various BioNano tools (including dependencies on BioNano IrysSolve packages) and requires GCC, Perl, and Python.