BiSCoT: improving large eukaryotic genome assemblies with optical maps

PeerJ

article

Benjamin Istace¹  Caroline Belser¹  Jean-Marc Aury¹ 

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

关键词: Genome assembly;    Bioinformatics;    Tool;    Scaffolding;    Optical maps;    Bionano;    Long reads;    Nanopore;    PacBio;   

DOI  :  10.7717/peerj.10150

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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

【 授权许可】

CC BY