contiBAIT

The 'contiBAIT' software tool addresses challenges in interpreting massively parallel sequencing data using Strand-seq information to repair and enhance existing reference assemblies. With the widespread use of massively parallel sequencing, reference assemblies are crucial, but many remain at intermediate stages of completion with scaffold builds or chromosome builds. 'contiBAIT,' implemented as an R package, leverages the information from Strand-seq data, which reveals template strand inheritance in single cells. This information helps determine the relative genomic distance and orientation between scaffolds, aiding in identifying and correcting errors within the assemblies.