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Background - The process of generating raw genome sequence data continues tobecome cheaper, faster, and more accurate. However, assembly of such data intohigh-quality, finished genome sequences remains challenging. Many genomeassembly tools are available, but they differ greatly in terms of theirperformance (speed, scalability, hardware requirements, acceptance of newerread technologies) and in their final output (composition of assembledsequence). More importantly, it remains largely unclear how to best assess thequality of assembled genome sequences. The Assemblathon competitions areintended to assess current state-of-the-art methods in genome assembly. Results- In Assemblathon 2, we provided a variety of sequence data to be assembled forthree vertebrate species (a bird, a fish, and snake). This resulted in a totalof 43 submitted assemblies from 21 participating teams. We evaluated theseassemblies using a combination of optical map data, Fosmid sequences, andseveral statistical methods. From over 100 different metrics, we chose ten keymeasures by which to assess the overall quality of the assemblies. Conclusions- Many current genome assemblers produced useful assemblies, containing asignificant representation of their genes, regulatory sequences, and overallgenome structure. However, the high degree of variability between the entriessuggests that there is still much room for improvement in the field of genomeassembly and that approaches which work well in assembling the genome of onespecies may not necessarily work well for another.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species