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Protocols

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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Versioning


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Documentation


Maintainer


  • person_outline Daniel R. Zerbino

Publications for Velvet

Velvet citations

 (1397)
library_books

The aquatic animals’ transcriptome resource for comparative functional analysis

2018
BMC Genomics
PMCID: 5954267
PMID: 29764375
DOI: 10.1186/s12864-018-4463-x

[…] 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 is n […]

call_split

Complete Sequence of the Intronless Mitochondrial Genome of the Saccharomyces cerevisiae Strain CW252

2018
Genome Announc
PMCID: 5920167
PMID: 29700138
DOI: 10.1128/genomeA.00219-18
call_split See protocol

[…] ith 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 to be chimeric, […]

call_split

Draft Genome Sequence of Multidrug Resistant Escherichia coli NIVEDI P44, Isolated from a Chicken Fecal Sample in Northeast India

2018
Genome Announc
PMCID: 5920187
PMID: 29700135
DOI: 10.1128/genomeA.00205-18
call_split See protocol

[…] -generation 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 annotation […]

library_books

Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution

2018
PLoS One
PMCID: 5919020
PMID: 29694430
DOI: 10.1371/journal.pone.0195994

[…] www.bioinformatics.bbsrc.ac.uk/projects/download.html). 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 to the scaffol […]

library_books

Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

2018
R Soc Open Sci
PMCID: 5936940
PMID: 29765675
DOI: 10.1098/rsos.172212

[…] Processed reads were assembled into contigs using Velvet v1.2.09 and assemblies for all odd-numbered k-mer lengths from 21 to 75 were evaluated. The expected k-mer coverage was determined for each assembly using the mode of a k-mer coverage histogram […]

library_books

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

2018
PLoS One
PMCID: 5919006
PMID: 29694416
DOI: 10.1371/journal.pone.0196069

[…] om the collected reads a de novo assembly was carried out with the built-in Geneious assembler platform with zero mismatches and gaps allowed among the reads. The similar procedure was conducted with Velvet v1.2.10 [] with k-mer length 37, minimum contig length 74 and default settings by applying a 400× upper coverage limit. The resulting contigs were then circularized by matching end points. The […]


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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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