BiSCoT: improving large eukaryotic genome assemblies with optical maps

Benjamin Istace; Caroline Belser; Jean-Marc Aury

doi:10.7717/peerj.10150

BiSCoT: improving large eukaryotic genome assemblies with optical maps

PeerJ. 2020 Nov 5:8:e10150. doi: 10.7717/peerj.10150. eCollection 2020.

Authors

Benjamin Istace¹, Caroline Belser¹, Jean-Marc Aury¹

Affiliation

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

Abstract

Motivation: Long read sequencing and Bionano Genomics optical maps are two techniques that, when used together, make it possible to reconstruct entire chromosome or chromosome arms structure. However, the existing tools are often too conservative and organization of contigs into scaffolds is not always optimal.

Results: We developed BiSCoT (Bionano SCaffolding COrrection Tool), a tool that post-processes files generated during a Bionano scaffolding in order to produce an assembly of greater contiguity and quality. BiSCoT was tested on a human genome and four publicly available plant genomes sequenced with Nanopore long reads and improved significantly the contiguity and quality of the assemblies. BiSCoT generates a fasta file of the assembly as well as an AGP file which describes the new organization of the input assembly.

Availability: BiSCoT and improved assemblies are freely available on GitHub at http://www.genoscope.cns.fr/biscot and Pypi at https://pypi.org/project/biscot/.

Keywords: Bioinformatics; Bionano; Genome assembly; Long reads; Nanopore; Optical maps; PacBio; Scaffolding; Tool.

Grants and funding

This work was supported by the Genoscope, the Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA) and France Génomique (ANR-10-INBS-09-08). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.