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Information


Unique identifier OMICS_01501
Name VAMPS
Alternative name Visualization and Analysis of Microbial Population Structures
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Visualization and Analysis of Microbial Population Structures

VAMPS citations

 (71)
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Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life

2018
Front Microbiol
PMCID: 5945997
PMID: 29780369
DOI: 10.3389/fmicb.2018.00840
call_split See protocol

[…] For this study, two versions of the CoDL dataset were obtained through the Visualization and Analysis of Microbial Population Structure web portal (VAMPS; ). The VAMPS web portal allows users to upload data and process using standardized pipelines. Using the VAMPS portal, two datasets were downloaded in May 2017. The first is a taxonomic identifi […]

library_books

Metaviz: interactive statistical and visual analysis of metagenomic data

2018
Nucleic Acids Res
PMCID: 5887897
PMID: 29529268
DOI: 10.1093/nar/gky136

[…] ol for exploring annotated pan genome datasets based on D3.js libraries (). Krona is a web-based tool for metagenomics visualization that provides a sunburst diagram to navigate the feature space (). VAMPS is a web service that provides a JavaScript and PHP-based metagenomics visualization toolkit of datasets uploaded by researchers (). Anvi’o is a multiomics platform that supports analysis using […]

library_books

Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient

2018
PeerJ
PMCID: 5935077
PMID: 29736349
DOI: 10.7717/peerj.4735

[…] ic assignments were performed using QIIME (pick_otus.py, method: uclust) (, ) and GAST (). Sequences are publicly available at the “The Visualization and Analysis of Microbial Population Structures” (VAMPS) website (https://vamps.mbl.edu/) () under project title: “JAH_TRP_Bv4v5” and are deposited at the NCBI SRA under accession number PRJNA384656. […]

call_split

Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic Associated Mortality in Fish

2017
mSystems
PMCID: 5675916
PMID: 29124129
DOI: 10.1128/mSystems.00133-17
call_split See protocol

[…] oduct in a second 10-cycle PCR using primers with Illumina HiSeq adaptors and barcodes attached to their 5′ end. Our fusion PCR protocols and primer sequences are further explained elsewhere (https://vamps.mbl.edu/resources/primers.php). Paired-end sequencing was conducted at the WM Keck Ecological and Evolutionary Genetics Facility at the Marine Biological Laboratory (MBL) using an Illumina HiSeq […]

library_books

Methane Dynamics in a Tropical Serpentinizing Environment: The Santa Elena Ophiolite, Costa Rica

2017
Front Microbiol
PMCID: 5440473
PMID: 28588569
DOI: 10.3389/fmicb.2017.00916

[…] variable regions of the 16S rRNA gene (518F-926R for bacteria and 517F-958R for archaea), following the methods described by Nelson et al. (). Quality-filtering of the sequences was conducted via the Visualization and Analysis of Microbial Population Structures (VAMPS) pipeline (Huse et al., ). These data are publicly available at https://vamps.mbl.edu/ under the project code DCO_BRZ and the sampl […]

library_books

Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia Oxidizing Archaea and Comammox Nitrospira

2017
Front Microbiol
PMCID: 5276851
PMID: 28194147
DOI: 10.3389/fmicb.2017.00101

[…] V4-V5 illumina MiSeq chemistries (Huse et al., ; Nelson et al., ). Reaction conditions and primers for all illumina runs are detailed in the aforementioned citations, and may be accessed at: https://vamps.mbl.edu/resources/primers.php#illumina. Sequence run processing and quality control for the V6 dataset are described in Fisher et al. (), while CutAdapt was used to trim the V4-V5 data of low qu […]

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VAMPS institution(s)
Department of Pathology and Laboratory Medicine, Brown University, Campus, Providence, RI, USA

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