ArticleBMC genomics2015
Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
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- Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data.Molecular ecology resources · 2025Article
- Interplay between large low-recombining regions and pseudo-overdominance in a plant genome.Nature communications · 2025Article
- Optical genome mapping reveals novel structural variations in an autism spectrum disorder cohort.Computational and structural biotechnology journal · 2025Article
- The black honey bee genome: insights on specific structural elements and a first step towards pangenomes.Genetics, selection, evolution : GSE · 2024Article
- A chromosome-level genome assembly ofFrontiers in plant science · 2024Article
- A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (Rissa tridactyla), a Declining Circumpolar Seabird.Genome biology and evolution · 2023Article
- An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.G3 (Bethesda, Md.) · 2023Article
- Detection of Transgene Location in the CYP2A13/2B6/2F1-transgenic Mouse Model using Optical Genome Mapping Technology.Drug metabolism and disposition: the biological fate of chemicals · 2023Article
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- HGGA: hierarchical guided genome assembler.BMC bioinformatics · 2022Article
- Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum.Science China. Life sciences · 2022Article
- Robust Benchmark Structural Variant Calls of An Asian Using State-of-the-art Long-read Sequencing Technologies.Genomics, proteomics & bioinformatics · 2022Article
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- A high-continuity and annotated tomato reference genome.BMC genomics · 2021Article
- Current status of structural variation studies in plants.Plant biotechnology journal · 2021Review
- A widely diverged locus involved in locomotor adaptation inScience advances · 2021Article
- Multicolor Whole-Genome Mapping in Nanochannels for Genetic Analysis.Analytical chemistry · 2021Article
- Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph.Algorithms for molecular biology : AMB · 2021Article
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Authors and funding
8 authors.
Funding
Abstract
backgroundGenome assembly remains an unsolved problem. Assembly projects face a range of hurdles that confound assembly. Thus a variety of tools and approaches are needed to improve draft genomes.
resultsWe used a custom assembly workflow to optimize consensus genome map assembly, resulting in an assembly equal to the estimated length of the Tribolium castaneum genome and with an N50 of more than 1 Mb. We used this map for super scaffolding the T. castaneum sequence assembly, more than tripling its N50 with the program Stitch.
conclusionsIn this article we present software that leverages consensus genome maps assembled from extremely long single molecule maps to increase the contiguity of sequence assemblies. We report the results of applying these tools to validate and improve a 7x Sanger draft of the T. castaneum genome.
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