BAIT

BAIT analyzes Strand-Seq data to map and visualize sister chromatid exchanges (SCEs) and infer parental DNA template-strand inheritance for detecting genomic instability and identifying reference genome assembly errors.

Key Features:

• DNA strand inheritance analysis: Analyzes DNA strand inheritance patterns using data derived from the Strand-Seq sequencing protocol.
• SCE mapping and visualization: Maps and visualizes sister chromatid exchanges (SCEs) from single-cell Strand-Seq data.
• Parental template-strand resolution: Independently sequences parental DNA template strands from single cells to reveal template-specific inheritance.
• High-resolution SCE detection: Detects SCE events with resolution reported up to 23 base pairs (bp).
• Reference assembly error detection: Identifies misoriented contigs and fragments in reference genomes, exemplified by discovery of at least 17 incorrectly oriented segments in the mm9 mouse assembly.
• Empirical SCE quantification: Reports empirical metrics such as an average of eight SCEs per murine embryonic stem (mES) cell and detection of misorientations representing nearly 1% of the genome in mm9.
• Species-specific input handling: Accepts species-specific Strand-Seq data to accommodate analyses across a range of species.

Scientific Applications:

• Genomic instability assessment: Uses SCE mapping as an indicator of genomic stress and instability.
• Reference genome refinement: Enables identification and correction of assembly errors such as misoriented contigs in reference genomes like mm9.
• Single-cell genomics: Enhances single-cell sequencing studies by revealing template-strand inheritance and high-resolution SCE events.
• Genomic integrity and evolution studies: Supports investigations into genomic integrity and evolutionary processes by detecting SCE patterns and assembly discrepancies.

Methodology:

Processes Strand-Seq sequencing data by independently sequencing parental DNA template strands from single cells and mapping and visualizing sister chromatid exchanges (SCEs), with detection reported at up to 23 bp resolution.