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QUAST specifications

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Unique identifier OMICS_02115
Name QUAST
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, Perl, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publications for QUAST

QUAST citations

 (564)
library_books

Draft Genome Sequences of Two Salmonella Strains Isolated from Wild Animals on the Eastern Shore of Virginia

2018
Genome Announc
PMCID: 5946047
PMID: 29748400
DOI: 10.1128/genomeA.00329-18

[…] spades version 3.9.0 (), and annotation of the draft genomes was performed using the ncbi prokaryotic genome annotation pipeline (pgap) ()., quality of the de novo assemblies was assessed using quast version 4.5 (). the n50 values of the two assemblies were 278,931 bp and 357,417 bp for va-wgs-00333 and va-wgs-00353, respectively. the gc content values (va-wgs-00333, 52.07%; va-wgs-00353, […]

library_books

Global evolution and phylogeography of Brucella melitensis strains

2018
BMC Genomics
PMCID: 5946514
PMID: 29747573
DOI: 10.1186/s12864-018-4762-2

[…] ; 20, as well as reids less than 75 nucleotides long were removed. the genome was assembled in the software newbler v 3.0 (roche). evaluation of the quality of genome assembly was performed using the quast 3.0 program [], the genomic sequence of b. melitensis 16 m strain (genebank: nc003317, nc003318) was used as a reference to evaluate the accuracy and efficiency of assembly of genomic projects. […]

library_books

Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

2018
Sci Rep
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] and k-values of 21, 33, 55, 77, 99, and 127. a second assembly excluding the k-value 127 was also performed to improve assemblies with shorter read lengths. assembly quality was evaluated with quast and the assembly with the fewest number of contigs and highest n50 was used in downstream analyses. additionally, plasmidspades was implemented with default settings to detect and assemble […]

library_books

Complex signatures of genomic variation of two non model marine species in a homogeneous environment

2018
BMC Genomics
PMCID: 5944137
PMID: 29743012
DOI: 10.1186/s12864-018-4721-y

[…] determined optimal k-mer lengths of 81 for the cape urchin and 91 for the granular limpet. assembly statistics, such as assembly length, longest contig, and n50 and l50 lengths were calculated with quast v4.1.1 []., as semi-global alignment and realignment of unmapped reads is recommended for pooled samples [], we used bwa-mem [], following the same parameters as in toonen et al. [], to map […]

library_books

The influence of oxygen and methane on nitrogen fixation in subarctic Sphagnum mosses

2018
PMCID: 5936483
PMID: 29730829
DOI: 10.1186/s13568-018-0607-2

[…] 8), a maximum of 2 differences with the primer sequence and minimum average quality score of 20 over a window of 50 base pairs. improved reads were aligned to the silva nr database (release v123) (quast et al. ). chimera’s were removed using uchime. next, reads were classified at bootstrap value of 80%, after which the unwanted and non-target lineages archaea, eukaryota, chloroplast, […]

library_books

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

2018
Front Microbiol
PMCID: 5945981
PMID: 29780368
DOI: 10.3389/fmicb.2018.00836

[…] were kept for de novo assembly, which was performed using spades genome assembler 3.10.1 algorithm (bankevich et al., ). the quality of each assembled genome was assessed following analysis with the quast software (gurevich et al., ) and all were satisfactory based on the number of contigs, size of the largest contig, number of bases in the assembly, and ng50 (data not shown). prophage sequences […]


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QUAST institution(s)
Algorithmic Biology Laboratory, St Petersburg Academic University, Russian Academy of Sciences, St Petersburg, Russia

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