contiBAIT

contiBAIT refines de novo genome assemblies by integrating Strand-seq single-cell strand inheritance data to detect and correct scaffold misorientations and mislocalizations and to cluster and order contigs into putative chromosomes.

Key Features:

• Implementation: Implemented as an R/Bioconductor package.
• Strand Inheritance Data Utilization: Uses Strand-seq single-cell strand inheritance data to establish relative orientations and distances between scaffolds.
• Error Correction: Identifies and corrects scaffold misorientations and mislocalizations arising from repetitive regions and sequencing errors.
• Chromosome-Level Assembly Improvement: Clusters unbridged contigs into putative chromosomes and orders scaffolds within chromosomes.
• Complementary Methodology: Provides orthogonal verification to conventional sequencing-based assemblies by leveraging strand inheritance signals.

Scientific Applications:

• De novo assembly refinement: Improves orientation and placement of scaffolds in de novo genome assemblies.
• Resolving complex regions: Helps resolve repetitive and structurally complex genomic regions that cause assembly errors in conventional sequencing.
• Chromosome-scale builds and downstream analyses: Facilitates generation of chromosome-scale builds and reduces structural assembly errors that affect downstream genetic analyses.

Methodology:

Integrates Strand-seq single-cell strand inheritance data with existing genome assemblies to infer relative genomic distances and orientations, detect misorientations and mislocalizations, cluster contigs into putative chromosomes, and order scaffolds within those chromosomes.