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Related Experiment Video

Updated: Nov 30, 2025

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Published on: June 28, 2012

BiSCoT: improving large eukaryotic genome assemblies with optical maps.

Benjamin Istace¹, Caroline Belser¹, Jean-Marc Aury¹

¹Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.

|November 16, 2020

Summary

This summary is machine-generated.

We developed BiSCoT, a tool that improves genome assembly quality by optimizing contig scaffolding. This Bionano Genomics optical map post-processing tool enhances contiguity and accuracy for long-read sequencing data.

Keywords:

Bioinformatics Bionano Genome assembly Long reads Nanopore Optical maps PacBio Scaffolding Tool

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Long-read sequencing and Bionano Genomics optical maps enable chromosome structure reconstruction.
Current scaffolding tools can be overly conservative, leading to suboptimal contig organization.

Purpose of the Study:

To develop a post-processing tool, BiSCoT, for optimizing Bionano Genomics scaffolding.
To enhance the contiguity and quality of genome assemblies.

Main Methods:

BiSCoT (Bionano SCaffolding COrrection Tool) post-processes Bionano scaffolding files.
The tool was tested on human and plant genomes sequenced with Nanopore long reads.

Main Results:

BiSCoT significantly improved the contiguity and quality of genome assemblies.
The tool generates FASTA and AGP files detailing the improved assembly organization.

Conclusions:

BiSCoT offers an effective solution for refining genome assemblies generated by long-read sequencing and optical mapping.
The software is freely available for research use.