GAGE: A critical evaluation of genome assemblies and assembly algorithms
Steven L. Salzberg,Adam M. Phillippy,Aleksey V. Zimin,Daniela Puiu,Tanja Magoc,Sergey Koren,Sergey Koren,Todd J. Treangen,Michael C. Schatz,Arthur L. Delcher,Michael Roberts,Guillaume Marçais,Mihai Pop,James A. Yorke +13 more
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TLDR
Evaluating several of the leading de novo assembly algorithms on four different short-read data sets generated by Illumina sequencers concludes that data quality, rather than the assembler itself, has a dramatic effect on the quality of an assembled genome.Abstract:
New sequencing technology has dramatically altered the landscape of whole-genome sequencing, allowing scientists to initiate numerous projects to decode the genomes of previously unsequenced organisms. The lowest-cost technology can generate deep coverage of most species, including mammals, in just a few days. The sequence data generated by one of these projects consist of millions or billions of short DNA sequences (reads) that range from 50 to 150 nt in length. These sequences must then be assembled de novo before most genome analyses can begin. Unfortunately, genome assembly remains a very difficult problem, made more difficult by shorter reads and unreliable long-range linking information. In this study, we evaluated several of the leading de novo assembly algorithms on four different short-read data sets, all generated by Illumina sequencers. Our results describe the relative performance of the different assemblers as well as other significant differences in assembly difficulty that appear to be inherent in the genomes themselves. Three overarching conclusions are apparent: first, that data quality, rather than the assembler itself, has a dramatic effect on the quality of an assembled genome; second, that the degree of contiguity of an assembly varies enormously among different assemblers and different genomes; and third, that the correctness of an assembly also varies widely and is not well correlated with statistics on contiguity. To enable others to replicate our results, all of our data and methods are freely available, as are all assemblers used in this study.read more
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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
TL;DR: An objective measure of genome quality is proposed that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities and is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches.
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QUAST: quality assessment tool for genome assemblies
TL;DR: This tool improves on leading assembly comparison software with new ideas and quality metrics, and can evaluate assemblies both with a reference genome, as well as without a reference.
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Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren,Brian P. Walenz,Konstantin Berlin,Jason R. Miller,Nicholas H. Bergman,Adam M. Phillippy +5 more
TL;DR: Canu, a successor of Celera Assembler that is specifically designed for noisy single-molecule sequences, is presented, demonstrating that Canu can reliably assemble complete microbial genomes and near-complete eukaryotic chromosomes using either Pacific Biosciences or Oxford Nanopore technologies.
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SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
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TL;DR: This work provides an updated assembly version of the 2008 Asian genome using SOAPdenovo2, a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.
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