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Assemblathon 1: a competitive assessment of de novo short read assembly methods.

ABSTRACT: 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/.

SUBMITTER: Earl D

PROVIDER: S-EPMC3227110 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature

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Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl Dent D Bradnam Keith K St John John J Darling Aaron A Lin Dawei D Fass Joseph J Yu Hung On Ken HO Buffalo Vince V Zerbino Daniel R DR Diekhans Mark M Nguyen Ngan N Ariyaratne Pramila Nuwantha PN Sung Wing-Kin WK Ning Zemin Z Haimel Matthias M Simpson Jared T JT Fonseca Nuno A NA Birol İnanç İ Docking T Roderick TR Ho Isaac Y IY Rokhsar Daniel S DS Chikhi Rayan R Lavenier Dominique D Chapuis Guillaume G Naquin Delphine D Maillet Nicolas N Schatz Michael C MC Kelley David R DR Phillippy Adam M AM Koren Sergey S Yang Shiaw-Pyng SP Wu Wei W Chou Wen-Chi WC Srivastava Anuj A Shaw Timothy I TI Ruby J Graham JG Skewes-Cox Peter P Betegon Miguel M Dimon Michelle T MT Solovyev Victor V Seledtsov Igor I Kosarev Petr P Vorobyev Denis D Ramirez-Gonzalez Ricardo R Leggett Richard R MacLean Dan D Xia Fangfang F Luo Ruibang R Li Zhenyu Z Xie Yinlong Y Liu Binghang B Gnerre Sante S MacCallum Iain I Przybylski Dariusz D Ribeiro Filipe J FJ Yin Shuangye S Sharpe Ted T Hall Giles G Kersey Paul J PJ Durbin Richard R Jackman Shaun D SD Chapman Jarrod A JA Huang Xiaoqiu X DeRisi Joseph L JL Caccamo Mario M Li Yingrui Y Jaffe David B DB Green Richard E RE Haussler David D Korf Ian I Paten Benedict B

Genome research 20110916 12

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 ...[more]

PMID: 21926179

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Project description:BACKGROUND: RNA-seq has shown huge potential for phylogenomic inferences in non-model organisms. However, error, incompleteness, and redundant assembled transcripts for each gene in de novo assembly of short reads cause noise in analyses and a large amount of missing data in the aligned matrix. To address these problems, we compare de novo assemblies of paired end 90 bp RNA-seq reads using Oases, Trinity, Trans-ABySS and SOAPdenovo-Trans to transcripts from genome annotation of the model plant Ricinus communis. By doing so we evaluate strategies for optimizing total gene coverage and minimizing assembly chimeras and redundancy. RESULTS: We found that the frequency and structure of chimeras vary dramatically among different software packages. The differences were largely due to the number of trans-self chimeras that contain repeats in the opposite direction. More than half of the total chimeras in Oases and Trinity were trans-self chimeras. Within each package, we found a trade-off between maximizing reference coverage and minimizing redundancy and chimera rate. In order to reduce redundancy, we investigated three methods: 1) using cap3 and CD-HIT-EST to combine highly similar transcripts, 2) only retaining the transcript with the highest read coverage, or removing the transcript with the lowest read coverage for each subcomponent in Trinity, and 3) filtering Oases single k-mer assemblies by number of transcripts per locus and relative transcript length, and then finding the transcript with the highest read coverage. We then utilized results from blastx against model protein sequences to effectively remove trans chimeras. After optimization, seven assembly strategies among all four packages successfully assembled 42.9-47.1% of reference genes to more than 200 bp, with a chimera rate of 0.92-2.21%, and on average 1.8-3.1 transcripts per reference gene assembled. CONCLUSIONS: With rapidly improving sequencing and assembly tools, our study provides a framework to benchmark and optimize performance before choosing tools or parameter combinations for analyzing short-read RNA-seq data. Our study demonstrates that choice of assembly package, k-mer sizes, post-assembly redundancy-reduction and chimera cleanup, and strand-specific RNA-seq library preparation and assembly dramatically improves gene coverage by non-redundant and non-chimeric transcripts that are optimized for downstream phylogenomic analyses.

Dataset Information

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Publications

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

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