VelvetOptimiser statistics

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Citations per year

Number of citations per year for the bioinformatics software tool VelvetOptimiser
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Protocols

VelvetOptimiser specifications

Information


Unique identifier OMICS_03552
Name VelvetOptimiser
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Maintainer


  • person_outline Simon Gladman

VelvetOptimiser citations

 (169)
library_books

Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain

2018
Antimicrob Agents Chemother
PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] lates were assigned to the main E. coli phylogenetic groups on the basis of their clustering in a neighbor-joining tree created from rMLST alleles. Sequences were assembled using Velvet (v1.2.10) and VelvetOptimiser (v2.2.4) software, with sampling of all odd kmer lengths from 21 to 149. The default optimization parameters were used, together with a minimum contig size of 200 bp and the scaffoldin […]

call_split

Culturing of female bladder bacteria reveals an interconnected urogenital microbiota

2018
Nat Commun
PMCID: 5908796
PMID: 29674608
DOI: 10.1038/s41467-018-03968-5
call_split See protocol

[…] ute, as previously described. Annotated assemblies were produced using the pipeline described previously. For each sample, sequence reads were used to create multiple assemblies using Velvet v1.2 and VelvetOptimiser v2.2.5 (https://github.com/tseemann/VelvetOptimiser). An assembly improvement step was applied to the assembly with the best N50 and contigs were scaffolded using SSPACE and sequence g […]

library_books

Lineage‐specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group

2018
Mol Ecol
PMCID: 5947300
PMID: 29509989
DOI: 10.1111/mec.14546

[…] HiSeq 2500 analyser (Illumina, San Diego, CA, USA). 100‐bp short read paired‐end data were assembled using the velvet version 1.2.08 de novo assembly algorithm (Zerbino & Birney, ), incorporating the velvetoptimiser protocol (version 2.2.4) (https://github.com/tseemann/VelvetOptimiser) for all odd k‐mer values from 21 to 99. Scaffolding was disabled, and the minimum output contiguous sequence asse […]

library_books

Genomic Surveillance of 4CMenB Vaccine Antigenic Variants among Disease Causing Neisseria meningitidis Isolates, UK, 2010–2016

2018
PMCID: 5875271
PMID: 29553330
DOI: 10.3201/eid2404.171480

[…] WGS was part of the Meningitis Research Foundation Meningococcus Genome Library initiative (). Genomes were assembled by using Velvet and VelvetOptimiser, uploaded to the PubMLST database, and annotated by using Neisseria Sequence Typing Database numbers (NEIS) for all loci. Analysis was undertaken by using the gene-by-gene approach wit […]

library_books

Sequence analysis of the potato aphid Macrosiphum euphorbiae transcriptome identified two new viruses

2018
PLoS One
PMCID: 5875755
PMID: 29596449
DOI: 10.1371/journal.pone.0193239

[…] applied SEED (1.2.1) [] to cluster the RNA reads, and then used Velvet/Oases (1.0.15/0.1.18) [] to assemble the resulting center reads in each cluster and the initial reads, respectively. We used the VelvetOptimiser (2.1.7) tool to find the best k-mer length for Velvet/Oases between 19 and 71. The Velvet/Oases with SEED pre-processing generated 22,137 contigs with an N50 value of 2,003bp. The N50 […]

library_books

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

2018
BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] .1.05 [] and SOAPInDel v.1.08 [] pipelines with HiSeq PE reads. Scaffolding was performed by SSPACE- LongRead [] using HiSeq MP reads.Filtered reads of re-sequenced isolates were assembled de novo by VelvetOptimiser v.2.2.5 []. The optimized k-mer, expected coverage and coverage cutoffs were obtained through iterative process for various k-mer (37 to 67). Gaps were minimized by GapFiller v.1.10 [] […]


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