BACKGROUND: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended 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 for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. CONCLUSIONS: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
BACKGROUND: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended 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 for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. CONCLUSIONS: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
Authors: Heather Bracken-Grissom; Allen G Collins; Timothy Collins; Keith Crandall; Daniel Distel; Casey Dunn; Gonzalo Giribet; Steven Haddock; Nancy Knowlton; Mark Martindale; Mónica Medina; Charles Messing; Stephen J O'Brien; Gustav Paulay; Nicolas Putnam; Timothy Ravasi; Greg W Rouse; Joseph F Ryan; Anja Schulze; Gert Wörheide; Maja Adamska; Xavier Bailly; Jesse Breinholt; William E Browne; M Christina Diaz; Nathaniel Evans; Jean-François Flot; Nicole Fogarty; Matthew Johnston; Bishoy Kamel; Akito Y Kawahara; Tammy Laberge; Dennis Lavrov; François Michonneau; Leonid L Moroz; Todd Oakley; Karen Osborne; Shirley A Pomponi; Adelaide Rhodes; Scott R Santos; Nori Satoh; Robert W Thacker; Yves Van de Peer; Christian R Voolstra; David Mark Welch; Judith Winston; Xin Zhou Journal: J Hered Date: 2014 Jan-Feb Impact factor: 2.645
Authors: Carol A Gilchrist; Stephen D Turner; Margaret F Riley; William A Petri; Erik L Hewlett Journal: Clin Microbiol Rev Date: 2015-07 Impact factor: 26.132
Authors: Sean Hoban; Joanna L Kelley; Katie E Lotterhos; Michael F Antolin; Gideon Bradburd; David B Lowry; Mary L Poss; Laura K Reed; Andrew Storfer; Michael C Whitlock Journal: Am Nat Date: 2016-08-15 Impact factor: 3.926