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Velvet specifications

Information


Unique identifier OMICS_00038
Name Velvet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2.10
Stability Stable
Maintained Yes

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  • person_outline Daniel R. Zerbino <>

Publications for Velvet

Velvet in pipelines

 (276)
2018
PMCID: 5773145
PMID: 29343217
DOI: 10.1186/s12864-018-4440-4

[…] shotgun strategy was used to produce 76-bp paired-end reads (400-bp insert size) and 50-bp mate-pair reads (3-kb insert size). the paired-end reads were assembled into longer contigs using velvet version 1.0.12 [], with an optimized k-mer size of 65. the pre-assemblies were used to construct scaffolds with the sspace program []., the c. cacaofunesta genes were predicted by combining […]

2018
PMCID: 5794953
PMID: 29437106
DOI: 10.1128/genomeA.01563-17

[…] sequencing of this clone, which generated 4,893,928 short-read sequences in pairs of about 300 bp, totaling 611.7 mb, with a g+c content of 35.28%. de novo genome assembly was performed using velvet version 1.2.10 (), and further downstream processing was performed. genome annotation was performed with the rapid annotations using subsystems technology (rast) server. overall, we obtained […]

2018
PMCID: 5805871
PMID: 29439033
DOI: 10.1128/genomeA.00022-18

[…] dneasy tissue kit (qiagen, inc., valencia, ca, usa). sequencing was performed on the illumina miseq platform, generating 294,464,639 raw fastq paired-end reads, and was de novo assembled using velvet version 1.2.09 (). the total sequence length was 5,325,727 bp, with 55× genome coverage, and the n50 was determined to be 67,510 bp., prodigal version 2.60, rnammer version 1.2, […]

2018
PMCID: 5805883
PMID: 29439045
DOI: 10.1128/genomeA.01531-17

[…] and sa12 were determined with whole-genome shotgun sequencing by using illumina technology. these sequences were quality processed and trimmed, and all quality-controlled reads were assembled using velvet () software. for gene prediction, the software tool prodigal () was used. genes coding for rrna and trna were identified using trnascan-se () and rnammer (). the genome size of la12 […]

2018
PMCID: 5808220
PMID: 25741336
DOI: 10.3389/fmicb.2018.00122

[…] of the appropriate genome was counted as % of the genome covered by nucleotide information from the mapped small rna reads. (b) de novo assembling of the deduplicated reads was performed using velvet with k-mer: 13, 15, 17 (zerbino and birney, ). the generated contigs were annotated by blast megablast (morgulis et al., ) to the refseq of ncbi., to compare consensus sequences of virus […]


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Velvet in publications

 (1786)
PMCID: 5954267
PMID: 29764375
DOI: 10.1186/s12864-018-4463-x

[…] had been removed in a previous step, the other read was also removed to synchronize the read pairs., to ensure more complete assembly, we used three de novo assembly tools: oases (v0.2.08, requiring velvet v1.2.09) [, ], soapdenovo-trans (release 1.02) [], and trinity (release 2013–02-25) [] that based on the de bruijn graphs. previous reports suggest that coverage in transcriptomes assembly […]

PMCID: 5920167
PMID: 29700138
DOI: 10.1128/genomeA.00219-18

[…] tophat2 () on the mitochondrial genome of the s. cerevisiae s288c parent strain; they were then sampled by trinity () to obtain an estimated coverage of 30×. an assembly of the genome obtained by velvet () with a k-mer size of 55 produced 34 contigs (n50, 3.7 kb), which were subsequently scaffolded by sspace () to obtain 10 contigs (n50, 57.5 kb). some of these scaffolds seemed […]

PMCID: 5920187
PMID: 29700135
DOI: 10.1128/genomeA.00205-18

[…] sequencing quality control (ngs qc) toolkit version 2.3 () was used to filter high-quality data for the genome assembly. a total of 11,499,584 reads were generated and assembled using the velvet assembler (version 1.2.10) (), yielding 216 contigs of 4,791,462 bp and an n50 value of 90,342 bp. the estimated complete genome size is 4.76 mb, with a g+c content of 50.65%. genome […]

PMCID: 5932639
PMID: 29755354
DOI: 10.3389/fphar.2018.00419

[…] (http://duk.sourceforge.net/), quality trimmed with the fastqx-toolkit fastqtrimmer to remove low quality reads (https://github.com/agordon/fastx_toolkit). sequencing data was first assembled using velvet v. 1.2.07 (zerbino and birney, ), and the resulted contigs were then scaffolded with allpaths v. r46652 (butler et al., )., the annotation of the strain yhl was performed using the national […]

PMCID: 5919020
PMID: 29694430
DOI: 10.1371/journal.pone.0195994

[…] to obtain the best assembled results, we employed two assembly software programs to assemble the genome of z.mobilis, including edena v3 [] and velvet [].these scaffolds were ordered relative to the genome of the z. mobilis strain zm4, using a combination of the contiguator [] and act 10.2.0 []. the illumina reads were remapped […]


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Velvet institution(s)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Velvet funding source(s)
This work was supported by European Molecular Biology Laboratory’s central funds, and the Intramural Research Program of the National Human Genome Research Institute.

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