ArticlePeerJ2020
BiSCoT: improving large eukaryotic genome assemblies with optical maps.
Article in PeerJ, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution.Plant biotechnology journal · 2026Article
- Chromosome-scale assembly of European flax (Linum usitatissimum L.) genotypes and pangenomic analysis provide genomic tools to improve breeding.BMC genomics · 2025Article
- On the way to diploidization and unexpected ploidy in the grass Sporobolus section Spartina mesopolyploids.Nature communications · 2025Article
- An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.G3 (Bethesda, Md.) · 2023Article
- Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding.GigaScience · 2022Article
- Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph.BMC bioinformatics · 2021Article
- Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing.Communications biology · 2021Article
- Using de novo assembly to identify structural variation of eight complex immune system gene regions.PLoS computational biology · 2021Article
- Article
- Population genomics of apricots unravels domestication history and adaptive events.Nature communications · 2021Article
- Long-read assembly of the Brassica napus reference genome Darmor-bzh.GigaScience · 2020Article
- Advances in optical mapping for genomic research.Computational and structural biotechnology journal · 2020Review
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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. 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/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.