Research graph
References from Advances in optical mapping for genomic research. Local targets link to admitted publications; unresolved targets remain external evidence.
Limitations of next-generation genome sequence assembly
10.1038/nmeth.1527 · 2011 · External reference
Repetitive DNA and next-generation sequencing: Computational challenges and solutions
2012 · External reference
Beware of mis-assembled genomes
10.1093/bioinformatics/bti769 · 2005 · External reference
Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software
10.1038/s41467-019-11146-4 · 2019 · External reference
The MaSuRCA genome assembler
2013 · External reference
SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
10.1089/cmb.2012.0021 · 2012 · External reference
SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
2012 · External reference
Using the Velvet de novo assembler for short-read sequencing technologies
10.1002/0471250953.bi1105s31 · 2010 · External reference
ABySS: A parallel assembler for short read sequence data
10.1101/gr.089532.108 · 2009 · External reference
Improvements in Genomic Technologies: Application to Crop Genomics
10.1016/j.tibtech.2017.02.009 · 2017 · External reference
Coming of age: Ten years of next-generation sequencing technologies
2016 · External reference
10.1186/s13059-020-1935-5
10.1186/s13059-020-1935-5 · External reference
Piercing the dark matter: Bioinformatics of long-range sequencing and mapping
10.1038/s41576-018-0003-4 · 2018 · External reference
Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology
10.1186/2047-217x-3-34 · 2014 · External reference
BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes
10.1111/pbi.12513 · 2016 · External reference
Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps
10.1038/s41477-018-0289-4 · 2018 · External reference
Startups use short-read data to expand long-read sequencing market
10.1038/nbt0515-433 · 2015 · External reference
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
2014 · External reference
How best to identify chromosomal interactions: A comparison of approaches
2017 · External reference
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
10.1038/nbt.2727 · 2013 · External reference
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
10.1038/ng.3802 · 2017 · External reference
Structural variation in the sequencing era
2019 · External reference
Unresolved reference
External reference
Detection and assembly of novel sequence insertions using Linked-Read technology
2019 · External reference
10.1126/science.8211116
10.1126/science.8211116 · External reference
Tools and pipelines for BioNano data: Molecule assembly pipeline and FASTA super scaffolding tool
10.1186/s12864-015-1911-8 · 2015 · External reference
Optical mapping and its potential for large-scale sequencing projects
10.1016/s0167-7799(99)01326-8 · 1999 · External reference
Optical mapping in plant comparative genomics
10.1186/s13742-015-0044-y · 2015 · External reference
Applications of optical DNA mapping in microbiology
2017 · External reference
Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces
10.1073/pnas.92.11.5164 · 1995 · External reference
Optical mapping of lambda bacteriophage clones using restriction endonucleases
1995 · External reference
Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules
1998 · External reference
A single-molecule barcoding system using nanoslits for DNA analysis
2007 · External reference
Unresolved reference
External reference
Optically mapping multiple bacterial genomes simultaneously in a single run
2011 · External reference
Using optical mapping data for the improvement of vertebrate genome assemblies
2015 · External reference
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)
2013 · External reference
An improved genome release (version Mt4.0) for the model legume Medicago truncatula
10.1186/1471-2164-15-312 · 2014 · External reference
OPTIMA: Sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis
10.1186/s13742-016-0110-0 · 2016 · External reference
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
2012 · External reference
Unresolved reference
External reference
DNA fluorocode: A single molecule, optical map of DNA with nanometre resolution
2010 · External reference
Modelling BioNano optical data and simulation study of genome map assembly
2018 · External reference
Modeling the relaxation of internal DNA segments during genome mapping in nanochannels
10.1063/1.4964927 · 2016 · External reference
High-Definition Electronic Genome Maps from Single Molecule Data
2017 · External reference
10.1186/s13742-015-0096-z
10.1186/s13742-015-0096-z · External reference
OMTools: A software package for visualizing and processing optical mapping data
2017 · External reference
10.1186/2047-217x-3-33
10.1186/2047-217x-3-33 · External reference
A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings
2015 · External reference
10.1101/285692
10.1101/285692 · External reference
Fast and accurate correction of optical mapping data via spaced seeds
10.1093/bioinformatics/btz663 · 2020 · External reference
Alignment of optical maps
10.1089/cmb.2006.13.442 · 2006 · External reference
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
10.1093/bioinformatics/btn102 · 2008 · External reference
Statistical significance of optical map alignments
10.1089/cmb.2011.0221 · 2012 · External reference
Efficient indexed alignment of contigs to optical maps
2014 · External reference
OMBlast: Alignment tool for optical mapping using a seed-and-extend approach
2017 · External reference
Maligner: A fast ordered restriction map aligner
10.1093/bioinformatics/btv711 · 2016 · External reference
Kohdista: An efficient method to index and query possible Rmap alignments
2019 · External reference
Multiple Sequence Alignment Using ClustalW and ClustalX
10.1002/0471250953.bi0203s00 · 2003 · External reference
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
10.1093/nar/gkh340 · 2004 · External reference
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
2013 · External reference
OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps
2019 · External reference
Genomic mapping by fingerprinting random clones: A mathematical analysis
10.1016/0888-7543(88)90007-9 · 1988 · External reference
Comparison of the two major classes of assembly algorithms: Overlap-layout-consensus and de-bruijn-graph
2012 · External reference
Toward Simplifying and Accurately Formulating Fragment Assembly
10.1089/cmb.1995.2.275 · 1995 · External reference
An Eulerian path approach to DNA fragment assembly
10.1073/pnas.171285098 · 2001 · External reference
10.1109/bibm.2017.8217958
10.1109/bibm.2017.8217958 · External reference
Genomics via optical mapping II: Ordered restriction maps
10.1089/cmb.1997.4.91 · 1997 · External reference
An algorithm for assembly of ordered restriction maps from single DNA molecules
10.1073/pnas.0604040103 · 2006 · External reference
Unresolved reference
External reference
A clone-free, single molecule map of the domestic cow (Bos taurus) genome
2015 · External reference
Next-generation mapping: A novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis
10.1186/s13073-017-0479-0 · 2017 · External reference
OMWare: A tool for efficient assembly of genome-wide physical maps
2016 · External reference
runBNG: A software package for BioNano genomic analysis on the command line
10.1093/bioinformatics/btx366 · 2017 · External reference
MapOptics: A light-weight, cross-platform visualization tool for optical mapping alignment
10.1093/bioinformatics/bty1013 · 2019 · External reference
BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data
10.1186/s12859-017-1735-4 · 2017 · External reference
10.1093/bioinformatics/btx437
10.1093/bioinformatics/btx437 · External reference
OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly
2013 · External reference
BiSCoT: Improving large eukaryotic genome assemblies with optical maps
2019 · External reference
Novo&Stitch: Accurate reconciliation of genome assemblies via optical maps
10.1093/bioinformatics/bty255 · 2018 · External reference
OMGS: Optical Map-Based Genome Scaffolding
2019 · External reference
AGORA: Assembly Guided by Optical Restriction Alignment
2012 · External reference
Aligning optical maps to de Bruijn graphs
10.1093/bioinformatics/btz069 · 2019 · External reference
10.1007/978-3-319-38782-6_6
10.1007/978-3-319-38782-6_6 · External reference
Misassembly detection using paired-end sequence reads and optical mapping data
2015 · External reference
Accurate detection of chimeric contigs via Bionano optical maps
10.1093/bioinformatics/bty850 · 2019 · External reference
Whole-genome shotgun optical mapping of Deinococcus radiodurans
1999 · External reference
A shotgun optical map of the entire Plasmodium falciparum genome
1999 · External reference
Improving the ostrich genome assembly using optical mapping data
2015 · External reference
Rapid construction of genome map for large yellow croaker (Larimichthys crocea) by the whole-genome mapping in BioNano Genomics Irys system
2015 · External reference
De novo assembly and phasing of a Korean human genome
2016 · External reference
Nanopore sequencing and assembly of a human genome with ultra-long reads
2018 · External reference
High-coverage sequencing and annotated assemblies of the budgerigar genome
10.1186/2047-217x-3-11 · 2014 · External reference
The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly
2018 · External reference
A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana)
2019 · External reference
A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system
10.1093/gigascience/giz122 · 2019 · External reference
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
2018 · External reference
A chromosome conformation capture ordered sequence of the barley genome
2017 · External reference
Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus
2020 · External reference
Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano, and Hi-C analysis
2020 · External reference
Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species
2019 · External reference
Optical nano-mapping and analysis of plant genomes
10.1007/978-1-4939-3622-9_9 · 2016 · External reference
Improved maize reference genome with single-molecule technologies
10.1038/nature22971 · 2017 · External reference
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model
2017 · External reference
Construction and comparison of three reference-quality genome assemblies for soybean
10.1111/tpj.14500 · 2019 · External reference
A reference-grade wild soybean genome
2019 · External reference
De novo assembly of a Chinese soybean genome
10.1007/s11427-018-9360-0 · 2018 · External reference
Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B
10.1007/s00122-018-3165-8 · 2018 · External reference
The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants
2019 · External reference
Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense
2019 · External reference
10.1038/nbt.4318
10.1038/nbt.4318 · External reference
Mapping and sequencing of structural variation from eight human genomes
2008 · External reference
Genome-wide structural variation detection by genome mapping on nanochannel arrays
2016 · External reference
Genome maps across 26 human populations reveal population-specific patterns of structural variation
10.1038/s41467-019-08992-7 · 2019 · External reference
Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer
2018 · External reference
10.1126/science.aar6343
10.1126/science.aar6343 · External reference
OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps
2017 · External reference
Unresolved reference
External reference
Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
1998 · External reference
Multi-locus sequence typing: A tool for global epidemiology
2003 · External reference
Lateral genetic transfer and the construction of genetic exchange communities
10.1111/j.1574-6976.2010.00261.x · 2011 · External reference
Optical mapping as a routine tool for bacterial genome sequence finishing
10.1186/1471-2164-8-321 · 2007 · External reference
Whole-genome mapping: A new paradigm in strain-typing technology
2013 · External reference
Haplotype phasing: Existing methods and new developments
10.1038/nrg3054 · 2011 · External reference
Comparative genomics as a tool to understand evolution and disease
10.1101/gr.157503.113 · 2013 · External reference
Recent advances in experimental whole genome haplotyping methods
2017 · External reference
Assembly and diploid architecture of an individual human genome via single-molecule technologies
10.1038/nmeth.3454 · 2015 · External reference
First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis)
2019 · External reference
Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
2019 · External reference
Chromosome-scale de novo assembly and phasing of a Chinese indigenous pig genome
2019 · External reference
Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
2019 · External reference
Sequence-specific fluorescent labeling of double-stranded DNA observed at the single molecule level
10.1093/nar/gng125 · 2003 · External reference
Enzyme-free optical DNA mapping of the human genome using competitive binding
2019 · External reference
Optical mapping discerns genome wide DNA methylation profiles
10.1186/1471-2199-9-68 · 2008 · External reference
Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays
10.1021/acsnano.8b03023 · 2018 · External reference
Long-read single-molecule maps of the functional methylome
10.1101/gr.240739.118 · 2019 · External reference
Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping
2020 · External reference
High-throughput single-molecule telomere characterization
10.1101/gr.222422.117 · 2017 · External reference
CRISPR-bind: a simple, custom CRISPR/dCas9-mediated labeling of genomic DNA for mapping in nanochannel arrays
2018 · External reference
Current strategies of polyploid plant genome sequence assembly
10.3389/fpls.2018.01660 · 2018 · External reference
Genome graphs and the evolution of genome inference
2017 · External reference
Fast and accurate genomic analyses using genome graphs
10.1038/s41588-018-0316-4 · 2019 · External reference
Goodbye reference, hello genome graphs
10.1038/s41587-019-0199-7 · 2019 · External reference
OMSim: a simulator for optical map data
10.1093/bioinformatics/btx293 · 2017 · External reference
