Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

Keywords

Linkage (software), Genome, Computational biology, DNA sequencing, Sequence assembly

References

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Cited by

• Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea)Jingqun Ao, Jia Li, Xinxin You — 2015
• Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an ExamplePasi Rastas, Federico C. F. Calboli, Baocheng Guo — 2015
• Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) GenomeHsin Yuan Tsai, Diego Robledo, Natalie R Lowe — 2016
• Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage MapsBen Sutherland, Thierry Gosselin, Éric Normandeau — 2016
• De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologiesMohaddeseh Mousavi, Chunfa Tong, Fenxiang Liu — 2016
• Improvement of the threespine stickleback (Gasterosteus aculeatus) genome using a Hi-C-based Proximity-Guided Assembly methodCatherine L. Peichel, Shawn Sullivan, Ivan Liachko — 2016
• Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora liniClaire Anderson, Muhammad Adil Khan, Ann‐Maree Catanzariti — 2016
• Towards integration of population and comparative genomics in forest trees.Pär K. Ingvarsson, Torgeir R. Hvidsten, Nathaniel R. Street — 2016
• Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future DirectionsSean Hoban, Joanna L. Kelley, Katie E. Lotterhos — 2016
• DEVELOPMENT OF GENOMIC RESOURCES FOR THE EVALUATION OF RED SNAPPER, AN EMERGING SPECIES CANDIDATE FOR MARINE AQUACULTURE AND STOCK ENHANCEMENTAdrienne Elise Norrell — 2016
• What are we missing about marine invasions? Filling in the gaps with evolutionary genomicsCraig D. H. Sherman, Katie E. Lotterhos, Mark F. Richardson — 2016
• The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest speciesAlexie Papanicolaou, Marc F. Schetelig, Peter Arensburger — 2016
• The genetic map of goldfish (Carassius auratus) provided insights to the divergent genome evolutions in the Cyprinidae familyYouyi Kuang, Xianhu Zheng, Chunyan Li — 2016
• A high‐resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distanceNathalie Pavy, Manuel Lamothe, Betty Pelgas — 2017
• Linkage Mapping and Comparative Genomics of Red Drum (Sciaenops ocellatus) Using Next-Generation SequencingChristopher M. Hollenbeck, David S. Portnoy, Dana L. Wetzel — 2017
• Applications of genotyping by sequencing in aquaculture breeding and geneticsDiego Robledo, Christos Palaiokostas, Luca Bargelloni — 2017
• SSR-enriched genetic linkage maps of bermudagrass (Cynodon dactylon × transvaalensis), and their comparison with allied plant genomesSameer Khanal, Changsoo Kim, Susan Auckland — 2017
• The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguityIgnazio Verde, Jerry Jenkins, Luca Dondini — 2017
• Crosslink: A fast, scriptable genetic mapper for outcrossing speciesRobert J. Vickerstaff, Richard J. Harrison — 2017
• Population Structure, Connectivity, and Phylogeography of Two Balistidae with High Potential for Larval Dispersal: Balistes capriscus and Balistes vetulaLuca Antoni — 2017

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