The eukaryotic genome, its reads, and the unfinished assembly

• Length, quality and production of affordable short NGS read sequences have significantly improved.
• A truly finished eukaryotic genome assembly is a rare achievement.
• Static genome assemblies are not needed for some biological analyses.
• We propose an alternative role for assemblies as dynamic views of the primary reads.

In recent years, readily affordable short read sequences provided by next-generation sequencing (NGS) have become longer and more accurate. This has led to a jump in interest in the utility of NGS-only approaches for exploring eukaryotic genomes. The concept of a static, ‘finished’ genome assembly, which still appears to be a faraway goal for many eukaryotes, is yielding to new paradigms. We here motivate an object-view concept where the raw reads are the main, fixed object, and assemblies with their annotations take a role of dynamically changing and modifiable views of that object.