QUAST pipeline

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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  • MetaQUAST

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Publications for QUAST

QUAST citations

 (16)
2018
PMCID: 5864415

[…] taxon against the total number of processed sequences. selected v. fischeri gdna-spiked samples were subjected to de novo assembly with spades 3.9 (34). the resulting contigs were qualified with quast 4.3 (35) and further scaffolded with ragout 1.2 (36) against the v. fischeri es114 reference genome (refseq accession no. gcf_000011805.1). the resulting draft genomes were aligned […]

2018
PMCID: 5828338

[…] and subsequently filtered using trimmomatic [33]. the center for genomic epidemiology (cge) website was used for online assembly by spades [34]. the assemblies were assessed using quast [35], and rast was used for annotation [36]. emm-type and mlst-profiles were identified as previously outlined [26], and novel mlst alleles and profiles were submitted to pubmlst […]

2018
PMCID: 5769438

[…] with default parameters [46]. prodigal [47] was used for gene recognition and translation with the specific parameters for metagenomic sequences. quality assemblies’ quantification was performed by quast software [48]. predicted genes were first annotated against the rescap database by best blast hit approach using blastn software [49]. to identify only the genes belonging to the rescap […]

2018
PMCID: 5764939

[…] 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 (6)., 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 […]

2017
PMCID: 5663730

[…] sequences. next, we assembled the reads de novo using spades2.4 (25). we optimized the assembly at various k-mer values and selected the optimal assembly using assembly statistics generated by quast2.3 (21). annotation of the ig locus was carried out in the same manner as described in the previous section., all annotated sequences are available at genbank under accession numbers […]

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

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