VICUNA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool VICUNA
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Tool usage distribution map

This map represents all the scientific publications referring to VICUNA per scientific context
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Associated diseases

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Protocols

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

Versioning


No version available

Publication for VICUNA

VICUNA citations

 (18)
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The second molecular epidemiological study of HIV infection in Mongolia between 2010 and 2016

2017
PLoS One
PMCID: 5731755
PMID: 29244859
DOI: 10.1371/journal.pone.0189605
call_split See protocol

[…] or 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 Mo […]

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Genome to genome analysis highlights the impact of the human innate and adaptive immune systems on the hepatitis C virus

2017
Nat Genet
PMCID: 5873514
PMID: 28394351
DOI: 10.1038/ng.3835
call_split See protocol

[…] inst 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 as the most […]

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A Comparison of Deformed Wing Virus in Deformed and Asymptomatic Honey Bees

2017
PMCID: 5371956
PMID: 28272333
DOI: 10.3390/insects8010028
call_split See protocol

[…] m BLAST database of DWV master variants type A (NC_004830.2 and Kakugo virus NC_005876.1), B (AY251269.2) and C (CEND01000001.1) database using an e value of 10e−05 to assemble DWV-like contigs using VICUNA which was specifically developed to deal with highly variable data. Read data were uploaded to the NCBI Sequence Read Archive under study number SRP095247.Viral contigs were imported into Genei […]

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High resolution sequencing of hepatitis C virus reveals limited intra hepatic compartmentalization in end stage liver disease

2017
PMCID: 5558612
PMID: 27531641
DOI: 10.1016/j.jhep.2016.07.048
call_split See protocol

[…] he 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 have been d […]

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Pharmacometabolomics Informs Viromics toward Precision Medicine

2016
Front Pharmacol
PMCID: 5081366
PMID: 27833560
DOI: 10.3389/fphar.2016.00411

[…] rial 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 to the overlap–lay […]

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Moku virus; a new Iflavirus found in wasps, honey bees and Varroa

2016
Sci Rep
PMCID: 5054524
PMID: 27713534
DOI: 10.1038/srep34983
call_split See protocol

[…] ur 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 plot […]


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

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