V-Phaser 2 statistics

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Protocols

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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Versioning


No version available

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 citations

 (8)
library_books

ViroFind: A novel target enrichment deep sequencing platform reveals a complex JC virus population in the brain of PML patients

2018
PLoS One
PMCID: 5779639
PMID: 29360822
DOI: 10.1371/journal.pone.0186945

[…] alignment data, referred to as SAM file and its binary version, referred to as BAM file. These files include information on all mapped reads and can be used to visualize viral reads. We also used the V-phaser 2 software module (V-phaser 2, Broad Institute) to identify viral variants (variant calling) as previously described []. Importantly, the differentiation of low-frequency variants from sequen […]

library_books

Role of HIV specific CD8+ T cells in pediatric HIV cure strategies after widespread early viral escape

2017
PMCID: 5679167
PMID: 28983013
DOI: 10.1084/jem.20162123

[…] was 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 in th […]

call_split

Association study between mannose binding lectin haplotypes and X gene mutation of hepatitis B virus from treatment naïve patients

2016
PMCID: 5191875
PMID: 27824315
DOI: 10.18632/aging.101097
call_split See protocol

[…] cted 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,wh […]

library_books

Comparison of Next Generation Sequencing Technologies for Comprehensive Assessment of Full Length Hepatitis C Viral Genomes

2016
J Clin Microbiol
PMCID: 5035407
PMID: 27385709
DOI: 10.1128/JCM.00330-16

[…] the 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). […]

library_books

Detection of Natural Resistance Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct Acting Antiviral Agents Naïve Patients

2016
Int J Mol Sci
PMCID: 5037695
PMID: 27618896
DOI: 10.3390/ijms17091416

[…] ion 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). […]

library_books

Combinations of Oseltamivir and T 705 Extend the Treatment Window for Highly Pathogenic Influenza A(H5N1) Virus Infection in Mice

2016
Sci Rep
PMCID: 4879667
PMID: 27221530
DOI: 10.1038/srep26742

[…] ned 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. Transition […]

Citations

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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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