BiSCoT: improving large eukaryotic genome assemblies with optical maps

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/.

[1]  Brent S. Pedersen,et al.  Nanopore sequencing and assembly of a human genome with ultra-long reads , 2017, Nature Biotechnology.

[2]  Sergey Koren,et al.  De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing[CC-BY] , 2017, Plant Cell.

[3]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[4]  Stéphane Deschamps,et al.  A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping , 2018, Nature Communications.

[5]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[6]  Stefan Engelen,et al.  de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer , 2016, bioRxiv.

[7]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[8]  F. Denoeud,et al.  Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps , 2018, Nature Plants.

[9]  Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information , 2019, GigaScience.

[10]  Rui Fan,et al.  The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis , 2019, Nature Communications.

[11]  David Stephen Horner,et al.  SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica) , 2018, bioRxiv.

[12]  Adam M. Phillippy,et al.  Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit , 2019, bioRxiv.