Current Options for Creating Genome Assemblies, and their Uses

The era of reference genome sequences could be considered to have begun when the laboratory of Fred Blattner published a series of papers on the Escherichia coli genome in the early 1990s.  Automated versions of the same Sanger method technology used for that effort were applied to sequence the human genome, announced in 2002.  This effort included many varied techniques and technologies including large insert clones, genetic and physical maps, and painstaking "finishing" procedures.  Technological advances leading to very inexpensive production of short sequence reads have now made reports of new genome sequence common to the point where the genome itself is not considered a notable event.  However, during the maturation of the technology, the overall quality of the final assembly has actually decreased, albeit by a smaller increment than the cost has diminished.  The emergence of long read technologies has led to a resurgence in creation of reference-quality genome assemblies, especially in bacteria but more recently for more complex organisms.  The field continues to change rapidly, but the present state of affairs will be discussed and the analyses enabled by reference-quality genome sequence, in contrast to the short contig-longer scaffold norm of the last 5 or 6 years, will be considered.