BiSCoT

BiSCoT improves contiguity and accuracy of genome assemblies produced by Bionano scaffolding by post-processing Bionano output files to merge contigs that share enzymatic labelling sites.

Key Features:

• Post-processing of Bionano output: Processes files produced during Bionano scaffolding to optimize the organization of contigs into scaffolds.
• Identification of enzymatic labelling sites: Detects enzymatic labelling sites on contigs derived from optical maps.
• Contig merging at shared labels: When two contigs share labels, merges them at their last shared labelling site to improve scaffold continuity and assembly accuracy.
• Integration of sequencing and optical map data: Leverages Nanopore long reads together with Bionano Genomics optical maps to facilitate reconstruction of chromosomes or chromosome arms.
• Output formats: Produces an improved assembly FASTA file and an AGP (A Golden Path) file describing the new assembly organization.
• Empirical validation: Demonstrated increases in contiguity and assembly quality on a human genome and four publicly available plant genomes sequenced with Nanopore long reads.

Scientific Applications:

• Genome assembly improvement: Reduces fragmentation and increases scaffold continuity for assemblies scaffolded with Bionano optical maps.
• Chromosome reconstruction: Supports reconstruction of whole chromosomes or chromosome arms by merging contigs using optical map labels and long reads.
• Comparative and evolutionary genomics: Provides higher-resolution assemblies suitable for comparative genomics and evolutionary studies.
• Functional genomics: Generates improved assemblies for downstream functional genomics analyses.

Methodology:

Post-processes files produced by Bionano scaffolding, detects enzymatic labelling sites on contigs, merges contigs at their last shared labelling site when present, leverages Nanopore long reads alongside Bionano Genomics optical maps, and outputs an updated FASTA assembly plus a corresponding AGP file.