QUAST: quality assessment tool for genome assemblies
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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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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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References
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"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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"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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