V-Phaser 2 statistics

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V-Phaser 2 specifications

Information


Unique identifier OMICS_00232
Name V-Phaser 2
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Xiao Yang <>

Additional information


V-Phaser is available at: https://www.broadinstitute.org/viral-genomics/v-phaser

Publications for V-Phaser 2

V-Phaser 2 in publications

 (7)
PMCID: 5679167
PMID: 28983013
DOI: 10.1084/jem.20162123

[…] annotated with the location of the epitopes of interest. the de novo assemblies were aligned using muscle () to the annotated reference to determine the location of the epitopes in each assembly. v-phaser 2 with default parameters was used to call variants () and v-profiler to call haplotypes () for the hla-associated epitopes. only haplotypes with greater than 1% frequency were included […]

PMCID: 5191875
PMID: 27824315
DOI: 10.18632/aging.101097

[…] to their corresponding consensus sequences by using mosaik and rc454. quality control and visualization of the coverage profiles were assessed with qualimap2. variant calling was performed using v-phaser 2 and v-profiler and mann-whitney u test was employed to compare the difference between two groups. the complexity of hbv quasispecies was estimated by following equation: s=−∑in=fi(lnfi)n,, […]

PMCID: 5035407
PMID: 27385709
DOI: 10.1128/JCM.00330-16

[…] assembly using mosaik v2.2.28 (http://gkno.me/pipelines.html#mosaik), and variants were called by v-phaser v2.0 (http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/v-phaser-2)., fastq file quality was assessed using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). sam files were created by mapping against 64 whole-genome hcv reference […]

PMCID: 5037695
PMID: 27618896
DOI: 10.3390/ijms17091416

[…] 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 (p-value ≤ 0.05)., the versant hcv genotype v2.0 assay (lipa, siemens, healthcare diagnostic inc., tarrytown, ny, usa) was used […]

PMCID: 4879667
PMID: 27221530
DOI: 10.1038/srep26742

[…] to their corresponding consensus sequencing by using mosaik. the quality of the alignment and visualization of the coverage profiles was assessed with qualimap. variant calling was assessed using v-phaser 2 and v-profiler. per-gene nucleotide snt values were obtained by using the formula , where pi is the frequency of a sequence variant and n is the length of the corresponding gene. […]


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V-Phaser 2 institution(s)
Broad Institute of MIT & Harvard, Cambridge, MA, USA
V-Phaser 2 funding source(s)
Supported in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No.: HHSN272200900018C.

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