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

By Keith R Bradnam, Joseph N. Fass, A. Alexandrov, Paul Baranay, Michael Bechner, .Inancc Birol, Sébastien Boisvert, Jarrod Chapman, Guillaume Chapuis, Rayan Chikhi and 118 more. GigaScience, 2013

725 citations recorded by the source corpus.

BackgroundThe 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.ResultsIn 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.ConclusionsMany 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.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/db386cdd1c0b99b29081be401406a689bb36a35d

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Citations in the corpus

Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, background): “In a recent evaluation of the most commonly used de novo genome assemblers to assemble the genomes of three vertebrate species (snake, bird, and fish) by Assemblathon, the authors recommended not to trust the results of any single assembly, nor place too much faith in a single metric of quality or a”
Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions (2016, neutral): “Multiple methods should be implemented in parallel and compared to achieve the best assembly (Earl et al. 2011; Bradnam et al. 2013).”
Structural Characterization of the glycoprotein GP2 Core Domain from the CAS Virus, a Novel Arenavirus-like Species (2013, background): “The recent sequencing of the boa constrictor genome will facilitate the identification of host factors involved in entry [36].”
Assessing genome assembly quality using the LTR Assembly Index (LAI) (2018, methodology): “(2013) (17) with parameter ‘n = 25’ that splits scaffolds into contigs when sequencing gaps reached 25 bp.”
Redundans: an assembly pipeline for highly heterozygous genomes (2015, neutral): “These include, number of contigs, N50, and genome completeness expressed as the ratio of the observed versus expected assembly size (18).”
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads (2014, methodology): “Key algorithms of Platanus and the results of the intensive evaluation of Platanas using both simulated data and real data, including those from highly heterozygous genomes and those used in the de novo assembly contest Assemblathon 2 (Bradnam et al. 2013), are described here.”
Piercing the dark matter: bioinformatics of long-range sequencing and mapping (2018, background): “…are characterized by high contiguity (typically measured by average or N50 contig size), high completeness (typically measured by the fraction of the genes or fraction of the genome represented) and correctness (typically measured by both base-level accuracy and structural accuracy) 24,25 .”
Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage (2015, neutral): “However, such assemblies tend to be highly fragmented when they are generated using sequencing reads shorter than common repeats (1-4).”
The Genome 10K Project: A Way Forward (2015, neutral): “, Reference 37), was evaluated favorably in Assemblathon 2 (8).”
Towards complete and error-free genome assemblies of all vertebrate species (2020, background): “-m INT minimum coverage [10] -M INT maximum coverage [400]”
Informed and automated k-mer size selection for genome assembly (2013, background): “In the ideal scenario of perfect coverage and error-free reads, the best value of k for assembly would be the read length.”
Applications of next-generation sequencing to the study of biological invasions (2015, methodology): “Results from these projects have highlighted the value of using a large range of metrics to fully assess assembly quality (Salzberg et al., 2012; Bradnam et al., 2013).”