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

Janna L. Fierst
2015 Frontiers in Genetics  
Frontiers website link: www.frontiersin.org Citation: Fierst JL(2015) Using linkage maps to correct and scaffold de novo genome assemblies: Methods, challenges and computational tools. ABSTRACT 2 Modern high-throughput DNA sequencing has made it possible to inexpensively produce 3 genome sequences, but in practice many of these draft genomes are fragmented and 4 incomplete. Genetic linkage maps based on recombination rates between physical markers 5 have been used in biology for over 100 years
more » ... nd a linkage map, when paired with a de novo 6 sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. 7 Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage 8 maps, outline the current challenges, review the available software tools and discuss new 9 mapping technologies. 10
doi:10.3389/fgene.2015.00220 pmid:26150829 pmcid:PMC4473057 fatcat:f5kf2ht4mjdsfg6rcltdvqfhti