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Journal ArticleDOI

QUAST: quality assessment tool for genome assemblies

15 Apr 2013-Bioinformatics (Oxford University Press)-Vol. 29, Iss: 8, pp 1072-1075
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.
Abstract: Summary: Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST—a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website.
Citations
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal ArticleDOI
TL;DR: Zdobnov et al. as discussed by the authors proposed a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content, and implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs.
Abstract: Motivation Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50. Results We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO. Availability and implementation Software implemented in Python and datasets available for download from http://busco.ezlab.org. Contact evgeny.zdobnov@unige.ch Supplementary information Supplementary data are available at Bioinformatics online.

7,747 citations

Journal ArticleDOI
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.
Abstract: Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.

5,788 citations


Cites background from "QUAST: quality assessment tool for ..."

  • ...The quality of isolate genomes has traditionally been evaluated using assembly statistics such as N50 (Salzberg et al. 2012; Gurevich et al. 2013), whereas singlecell and metagenomic studies have relied on the presence and absence of universal single-copy “marker” genes for estimating genome…...

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  • ...The quality of isolate genomes has traditionally been evaluated using assembly statistics such as N50 (Salzberg et al. 2012; Gurevich et al. 2013), while single cell and metagenomic studies have relied on the presence and absence of universal single-copy ‘marker’ genes for estimating genome completeness (Wrighton et al....

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  • ...The quality of isolate genomes has traditionally been evaluated using assembly statistics such as N50 (Salzberg et al. 2012; Gurevich et al. 2013), whereas singlecell and metagenomic studies have relied on the presence and absence of universal single-copy “marker” genes for estimating genome completeness (Wrighton et al. 2012; Haroon et al. 2013; Rinke et al. 2013; Sharon et al. 2013)....

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  • ...This size range was selected because it approximates the contig lengths of genomes recovered from metagenomic data or singlecell genomics: The mean N50 of the GEBA-MDM single-cell genomes, Wrighton acetate-amended aquifer population genomes, and Sharon infant gut population genomes is ∼28 kbp, ∼17 kbp, and∼ 12 kbp, respectively....

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09 Jan 2016
TL;DR: This work proposes a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content, implemented in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO.
Abstract: MOTIVATION Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50. RESULTS We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO. AVAILABILITY AND IMPLEMENTATION Software implemented in Python and datasets available for download from http://busco.ezlab.org. CONTACT evgeny.zdobnov@unige.ch SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

4,036 citations


Cites methods from "QUAST: quality assessment tool for ..."

  • ...Please send questions (after reading this user guide) to: support@orthodb.org Copyright © 2016 University of Geneva Medical School / Swiss Institute of Bioinformatics....

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Journal ArticleDOI
TL;DR: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner and generated a three-time larger assembly, with longer contig N50 and average contig length.
Abstract: Summary: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and without a GPU, respectively. MEGAHIT assembles the data as a whole, i.e., no pre-processing like partitioning and normalization was needed. When compared with previous methods (Chikhi and Rizk, 2012; Howe, et al., 2014) on assembling the soil data, MEGAHIT generated a 3-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a 4-fold improvement . Availability: The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license. Contact: rb@l3-bioinfo.com, twlam@cs.hku.hk

3,634 citations

References
More filters
Journal ArticleDOI
TL;DR: SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies.
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.

16,859 citations

01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal ArticleDOI
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
Abstract: We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25-50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of approximately 8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.

9,389 citations


"QUAST: quality assessment tool for ..." refers methods in this paper

  • ...However, both SPAdes and IDBA-UD have more misassemblies than the three Velvet-based assemblers....

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  • ...EþV-SC, Velvet and Velvet-SC generated assemblies with dozens of similar contigs; this is natural because all of these assemblers are modifications of Velvet....

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  • ...We also include several recently introduced assemblers that have been adapted or designed from scratch to handle single-cell datasets: Velvet-SC and EULERþVelvet-SC (Chitsaz et al., 2011), our assembler, SPAdes (Bankevich et al., 2012) and IDBA-UD (Peng et al., 2012)....

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  • ...We include several well-known assemblers designed for cultured bacterial datasets: EULER-SR (Pevzner et al., 2001), Velvet (Zerbino and Birney, 2008), and SOAPdenovo (Li et al., 2010)....

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  • ...Velvet was not able to assemble low-coverage regions of the genome, whereas the assemblers designed for single-cell datasets (Velvet-SC, EþV-SC, SPAdes and IDBA-UD) did much better, although, of course, none of them can assemble the regions that literally have zero coverage....

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Journal ArticleDOI
05 Sep 1997-Science
TL;DR: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident.
Abstract: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.

7,723 citations

Journal ArticleDOI
TL;DR: The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes.
Abstract: The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewing tools provide alternative ways to analyze genome alignments. The new system is the first version of MUMmer to be released as open-source software. This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at http://www.tigr.org/software/mummer.

4,886 citations


"QUAST: quality assessment tool for ..." refers background in this paper

  • ...Different assembly programs use different heuristic approaches to tackle these challenges, resulting in many differences in the contigs they output....

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