VelvetOptimiser protocols

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VelvetOptimiser specifications

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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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  • person_outline Simon Gladman <>

VelvetOptimiser in pipelines

 (7)
2017
PMCID: 5567929
PMID: 28861452
DOI: 10.1016/j.dib.2017.07.064

[…] final assembly was carried out using oases v0.2.08 (http://www.ebi.ac.uk/~/zerbino/oases/) . the appropriate k-mer and coverage cut-off value used in the assembly was determined by a perl script (velvetoptimiser-2.2.0.pl). k-mer size range from 75 to 89 were tested for the best n50 value while the coverage cut-off was automatically determined by the script. all other parameters […]

2017
PMCID: 5580483
PMID: 28812996
DOI: 10.3390/v9080226

[…] reads were aligned to their respective reference (bwa-mem, single end) with the resulting sam alignment file parsed to include only reads aligning uniquely. simulated reads were assembled using the velvetoptimiser perl script with the resulting assemblies evaluated using quast, as was carried out for the non-simulated reads., for this study, two hsv1 strains were sequenced. hsv1 strain 17syn+ […]

2016
PMCID: 4783777
PMID: 26955886
DOI: 10.1038/srep22794

[…] step size 2, q score 20), kmernator (k-mer size 31) and velvetoptimizer implemented in the galaxy platform provided by the gene centre, lmu, munich, germany. the following parameters were used in velvetoptimiser: start hash length 35, end hash length 85, no. of threads 4, k-mer optimization metric n50. resulting contigs were mapped onto the reference chromosomes with burrows-wheeler aligner […]

2016
PMCID: 5073307
PMID: 27767055
DOI: 10.1038/srep35776

[…] more than 50% of the single end sequencing read length are under score 5) from the raw data using fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). the reference sequence was assembled by velvetoptimiser assembler (settings: -s 23 -e 31 -x 4)., sequence readings from all five samples were aligned with the reference sequence using bwa software (v0.7.8, settings: aln -o 1 -m 100000 -t 4 […]

2016
PMCID: 5121376
PMID: 27629899
DOI: 10.1128/JCM.00881-16

[…] isolates were sequenced on an illumina hiseq sequencer (wellcome trust center for human genetics, university of oxford, uk). the resulting short-read sequences were assembled de novo using the velvetoptimiser algorithm () as part of an in-house pipeline developed in oxford and then added to the publicly accessible neisseria pubmlst website () (http://pubmlst.org/neisseria/), which uses […]


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VelvetOptimiser in publications

 (198)
PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] 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 […]

PMCID: 5908796
PMID: 29674608
DOI: 10.1038/s41467-018-03968-5

[…] 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 […]

PMCID: 5947300
PMID: 29509989
DOI: 10.1111/mec.14546

[…] 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 […]

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

[…] venipuncture, or small-volume pediatric blood cultures., 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 […]

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

[…] 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 […]


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