QUAST protocols

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QUAST computational protocol

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

 (26)
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 (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 […]

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

[…] 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: 5864415
PMID: 29577086
DOI: 10.1128/mSystems.00218-17

[…] 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 […]

2017
PMCID: 5331511
PMID: 28183771
DOI: 10.1128/genomeA.01617-16

[…] spain) using illumina paired-end sequencing technology. the quality of the reads was analyzed using trimmomatic version 0.32 (5). genome assembly was performed using spades version 3.6.1 (6), and quast (7). the resulting genome for lft 1.7 consists of 451 contigs (>200 bp) of 3,617,612 bp and has a g+c content of 28.7%. the n50 contig size was 343,594 bp, with the largest contig […]

2017
PMCID: 5383892
PMID: 28385844
DOI: 10.1128/genomeA.00125-17

[…] of 300 bp. the data are presented in table 1. sequence reads were trimmed and assembled de novo with clc genomics workbench version 8 (clc bio, aarhus, denmark). assembly quality was assessed using quast version 3.1 (5). following trimming, the average length of reads was 245 bp. the genome sequences were annotated using the ncbi prokaryotic genome annotation pipeline (pgap) (6). the statistics […]

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

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