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Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Genome Res. 2011 Dec; 21(12):2224-41
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15 Nov 2011
Arnab Pain
F1000 Microbiology
King Abdullah University of Science and Technology,
Thuwal, Mekkah, Saudi Arabia.
F1000 Microbiology
King Abdullah University of Science and Technology,
Thuwal, Mekkah, Saudi Arabia.
Grant Hill-Cawthorne
F1000 Microbiology
King Abdullah University of Science and Technology,
Thuwal, Mekkah, Saudi Arabia.
F1000 Microbiology
King Abdullah University of Science and Technology,
Thuwal, Mekkah, Saudi Arabia.
Technical Advance
DOI: 10.3410/f.13369986.14740101
In Assemblathon 1, Earl et al. bring together genome assembly teams from all of the major sequencing centres to demonstrate the accuracy of their pipelines in open competition. This is an excellent demonstration of collaborative science spurred on by a little competitive spirit and produces real life...Continue reading
In Assemblathon 1, Earl et al. bring together genome assembly teams from all of the major sequencing centres to demonstrate the accuracy of their pipelines in open competition. This is an excellent demonstration of collaborative science spurred on by a little competitive spirit and produces real life results that the rest of us can apply to our genome assembly problems.
As the majority of de novo sequencing projects are now going to be using 'short read' sequencing technologies in their entirety, we need to know which pieces of software, from the myriad available, can be combined into a pipeline to produce accurate and consistent results. Most reviews in this area have focused on comparing individual assembly algorithms or programs rather than whole multi-stage pipelines. Earl et al.'s approach was to encourage participating sequencing centres to apply their gold standard pipeline to an assembly challenge and, in turn, they developed indicators that could be used to evaluate these assemblies.
Altogether this led to 41 different assemblies from 17 different groups from around the world. Reassuringly, after looking at seven different metrics, N50 still appears to correlate well with more sophisticated measures of path and contiguity. It is clear though that success in one category often requires a trade-off cost in other categories. Therefore, there is still a vacancy for the perfect de novo assembly pipeline.
This paper represents an important collaborative effort. With high-throughput genome sequencing now done in many labs and not just at the big sequencing centres, we can use this strength in numbers to drive development forward. This paper marks the first step in further collaboration and friendly competition. Assemblathon 2 has already finished and the organisers have received 43 completed assemblies. This time the genomes are the Lake Malawi cichlid fish, boa constrictor and budgerigar. Much bigger challenges, but we shall soon see if further methodological gains can be made on the back of a good-natured competition.
As the majority of de novo sequencing projects are now going to be using 'short read' sequencing technologies in their entirety, we need to know which pieces of software, from the myriad available, can be combined into a pipeline to produce accurate and consistent results. Most reviews in this area have focused on comparing individual assembly algorithms or programs rather than whole multi-stage pipelines. Earl et al.'s approach was to encourage participating sequencing centres to apply their gold standard pipeline to an assembly challenge and, in turn, they developed indicators that could be used to evaluate these assemblies.
Altogether this led to 41 different assemblies from 17 different groups from around the world. Reassuringly, after looking at seven different metrics, N50 still appears to correlate well with more sophisticated measures of path and contiguity. It is clear though that success in one category often requires a trade-off cost in other categories. Therefore, there is still a vacancy for the perfect de novo assembly pipeline.
This paper represents an important collaborative effort. With high-throughput genome sequencing now done in many labs and not just at the big sequencing centres, we can use this strength in numbers to drive development forward. This paper marks the first step in further collaboration and friendly competition. Assemblathon 2 has already finished and the organisers have received 43 completed assemblies. This time the genomes are the Lake Malawi cichlid fish, boa constrictor and budgerigar. Much bigger challenges, but we shall soon see if further methodological gains can be made on the back of a good-natured competition.
Disclosures
None declared
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Pain A and Hill-Cawthorne G: F1000Prime Recommendation of [Earl D et al., Genome Res 2011, 21(12):2224-41]. In F1000Prime, 15 Nov 2011; DOI: 10.3410/f.13369986.14740101. F1000Prime.com/13369986#eval14740101
F1000Prime Recommendations, Dissents and Comments for [Earl D et al., Genome Res 2011, 21(12):2224-41]. In F1000Prime, 23 May 2013; F1000Prime.com/13369986
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Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.
PMID: 21926179
