AUTHOR=Fierst Janna L. 

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

JOURNAL=Frontiers in Genetics

VOLUME=6

YEAR=2015

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2015.00220

DOI=10.3389/fgene.2015.00220

ISSN=1664-8021

ABSTRACT=<p>Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a <italic>de novo</italic> sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating <italic>de novo</italic> assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies.</p>