VICUNA protocols

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VICUNA specifications

Information


Unique identifier OMICS_02162
Name VICUNA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for VICUNA

VICUNA in pipelines

 (4)
2017
PMCID: 5873514
PMID: 28394351
DOI: 10.1038/ng.3835

[…] a blastn database containing 165 hcv genomes covering its diversity both to choose an appropriate reference and to select those reads which formed a majority population for de novo assembly with vicuna v1.3 and finishing with v-fat v1.0 (http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/v-fat). population consensus sequence at each site is defined […]

2016
PMCID: 4820869
PMID: 27051465
DOI: 10.1186/s13040-016-0090-8

[…] should have only one genome. thus, such assemblers are generally not able to assemble reads that are related to but different from the majority reads. 3) some assembly programs (such as trinity, vicuna, cufflinks or predicthaplo) [] do indeed consider the possibility of multiple isoforms during de novo assembly and have the ability to produce multiple contigs []. however, in our experience […]

2016
PMCID: 5037695
PMID: 27618896
DOI: 10.3390/ijms17091416

[…] online: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and pre-processing with the pollux error correction software [], a de novo assembly was performed using software packages vicuna [] and v-fat []. the sample-specific majority rule consensus sequences were used to infer the variant frequencies with v-phaser 2 [], and we only considered variants that had no strand bias […]

2016
PMCID: 5041021
PMID: 27490575
DOI: 10.3390/vaccines4030027

[…] database containing all 165 hcv genomes [] covering its diversity both to choose an appropriate reference and to select those reads which formed a majority population for de novo assembly with vicuna v1.3 [] and finishing with v-fat v1.0 (http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/v-fat). reads were mapped back to the assembly using mosaik v2.2.28 […]


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VICUNA in publications

 (21)
PMCID: 5731755
PMID: 29244859
DOI: 10.1371/journal.pone.0189605

[…] the data obtained from miseq, trimming and filtering of the sequence data was conducted by the fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html), de novo assembly was conducted by vicuna [] and mapping was conducted by bwa-mem []. the time to the most recent common ancestor (tmrca) was estimated by maximum clade credibility (mcc) tree analysis using the bayesian markov chain […]

PMCID: 5873514
PMID: 28394351
DOI: 10.1038/ng.3835

[…] a blastn database containing 165 hcv genomes covering its diversity both to choose an appropriate reference and to select those reads which formed a majority population for de novo assembly with vicuna v1.3 and finishing with v-fat v1.0 (http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/v-fat). population consensus sequence at each site is defined […]

PMCID: 5558612
PMID: 27531641
DOI: 10.1016/j.jhep.2016.07.048

[…] manufacturer’s protocol. samples were pooled and sequenced on an illumina miseq platform, using a 2 × 250 bp v2 reagent kit. paired-end reads were assembled into a hcv consensus sequence using the vicuna de novo assembler software and finished with v-fat v1.0. reads were mapped back to the consensus using mosaik v2.1.73, and intra-host variants called by v-phaser v2.0 , . all reads […]

PMCID: 5081366
PMID: 27833560
DOI: 10.3389/fphar.2016.00411

[…] shotgun metagenomic projects (; ; ). yet, it remains to be determined, if newbler will be discontinued with the 454/roche in 2016 (). minimo is designed for the assembly of small datasets () and vicuna is an assembler that is specialized in de novo assembly of data from heterogeneous viral populations (). metavelvet () and other de brujin graph assemblers are an alternative […]

PMCID: 5054524
PMID: 27713534
DOI: 10.1038/srep34983

[…] joining method and the jukes-cantor genetic distance model based on the conserved rdrp region of picorna-like viruses. finally, geneious was used to map reads against the putative virus contig and vicuna was used to assemble reads from each individual separately using a pipeline adapted from assembling dwv., individual reads were aligned against the novel moku virus genome to create coverage […]


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VICUNA institution(s)
The Broad Institute of MIT and Harvard, Cambridge, MA, USA

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