Velvet 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 No

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Publications for Velvet

Velvet IN pipelines

 (107)
2018
PMCID: 5897803
PMID: 29650582
DOI: 10.1128/genomeA.00290-18

[…] of 422 to 502 bp (average size, ∼458 bp). all strains were sequenced using the illumina hiseq 4000 platform (illumina, inc., usa). sequences were trimmed using bbduk and de novo assembled using velvet 1.2.10, with the k-mer length set at 99 (22). contigs were reorganized by aligning to the genome sequence of the reference s. pseudintermedius strain 081661 (genbank accession no. nzcp016073) […]

2018
PMCID: 5829208
PMID: 29445022
DOI: 10.1098/rspb.2017.2732

[…] were then imported into clc genomics workbench version 7.0 (clc, aarhus, denmark) and de-multiplexed by barcode identity (genbank sra samn08384409 - samn0838442) and assembled into contigs using velvet version 1.2.10 [30] (see electronic supplementary material, methods for detailed methods). sequencing statistics are detailed in electronic supplementary material, table s4., to establish […]

2018
PMCID: 5843727
PMID: 29519841
DOI: 10.1128/genomeA.00148-18

[…] sequenced by the solexa genome analyzer at the beijing genome institution (bgi; shenzhen, china). a total of 6,045,713 clean paired-end reads were obtained. genome assembly was performed using the velvet assembly software package (11). the assembled contig, representing the entire tnav-6b genome sequence, was confirmed by six restriction enzyme digestion profiles (bamhi, ecori, hindiii, psti, […]

2018
PMCID: 5882929
PMID: 29615698
DOI: 10.1038/s41598-018-23807-3

[…] deep-sequencing using the illumina platform. sequenced reads match with the host p. digitatum databases (isolate pd1) were expurgated and the remaining reads were de novo assembled using velvet (version 1.2.10) with default parameters40. all contigs were subjected to blastn and blastx alignments against the ncbi database to search for viral sequences. the 5′- and 3′-terminal […]

2018
PMCID: 5794934
PMID: 29437087
DOI: 10.1128/genomeA.01223-17

[…] kit, according to the manufacturer’s instructions. the number of paired reads per sample ranged from 941,320 to 1,389,798. the average g+c content was 52.5% (8). de novo assembly was performed using velvet 1.2.10 set at default for all parameters (9). contigs were organized by aligning to the genome sequence of the reference strain s. typhimurium lt2 (accession no. nc_003197) using mauve […]

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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