QUAST protocols

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QUAST specifications

Information


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 in pipelines

 (88)
2018
PMCID: 5764930
PMID: 29326206
DOI: 10.1128/genomeA.01369-17

[…] using sickle (v1.33) (https://github.com/najoshi/sickle). subsequently, the quality-filtered reads were de novo assembled using spades (v3.9.0) (). final genome assemblies were analyzed using quast (v4.3) (), resulting in 43 to 197 contigs of >1 kb, and accounting for total genome sizes ranging from 4,578,015 to 5,285,335 bp (). coding sequences (cdss) and orthologous genes […]

2018
PMCID: 5764939
PMID: 29326215
DOI: 10.1128/genomeA.01430-17

[…] scaffolds shorter than 500 bp, unlikely to contain complete coding sequences, were removed. the 36.12-mb genome resulted from the assembly of 599 contigs. gc content was of 46.22% as assessed by quast ()., the draft genome sequence of t. adpressus a-t1c-84x (=cbs 142503) has been deposited at ddbj/ena/genbank under accession number nhzs00000000. the version described in this paper is version […]

2018
PMCID: 5769438
PMID: 29335005
DOI: 10.1186/s40168-017-0387-y

[…] with default parameters []. prodigal [] was used for gene recognition and translation with the specific parameters for metagenomic sequences. quality assemblies’ quantification was performed by quast software []. predicted genes were first annotated against the rescap database by best blast hit approach using blastn software []. to identify only the genes belonging to the rescap database […]

2018
PMCID: 5798813
PMID: 29423234
DOI: 10.1038/s41438-017-0011-0

[…] to ncbi under bioproject id prjna376668, designated ucd10x assembly v1.0. assembly statistics through each step of the analysis from contigs to scaffolds to pseudomolecules were calculated., quast (version 4.1) was utilized to simultaneously compare the ucd10x assembly v1.0 with three published c. annuum sequences, cm334 v1.55, zunla-1 v2.0, and chiltepin v2.0. default parameters […]

2018
PMCID: 5808120
PMID: 29468143
DOI: 10.3389/fcimb.2018.00025

[…] reference for mapping of all the single metagenomes, including those obtained with the ion torrent pgm. the quality of the cross-assembled scaffolds was evaluated using the quality assessment tool (quast) v4.5 (http://quast.sourceforge.net/) (gurevich et al., ). quast provides assembly statistics including the number of assembled contigs, the length of the longest contig and the values of n50, […]


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QUAST in publications

 (539)
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, […]

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. […]

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 […]

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 […]

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, […]


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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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