VizBin protocols

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VizBin specifications

Information


Unique identifier OMICS_11822
Name VizBin
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data Metagenomic fragments of interest
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Parallelization OpenMP
License BSD 3-clause “New” or “Revised” License
Computer skills Medium
Stability Stable
Requirements
BLAS/LAPACK
Maintained Yes

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Maintainer


  • person_outline Paul Wilmes <>

Publication for VizBin

VizBin in pipelines

 (3)
2018
PMCID: 5867873
PMID: 29518047
DOI: 10.3390/genes9030152

[…] was performed with metabat v0.26.3 []. checkm v1.0.5 [] was then used for assessment of completion and contamination of the extracted genomes or bins. further refinement of bins was carried out with vizbin v0.9 []. their taxonomic affiliation was determined by constructing a genomic tree with fasttree v2.1.3 [] of the concatenation of phylosift v.1.0.1 [] set of conserved genes […]

2017
PMCID: 5331489
PMID: 28183779
DOI: 10.1128/genomeA.01307-16

[…] swinhoei was collected near yongxing island (112°20′e, 16°50′n) in the south china sea. dna extraction, illumina sequencing, and metagenome assembling were carried out as described by liu et al. (). vizbin was used to extract the metagenomic bins from the metagenome contigs, using default settings (). contigs shorter than 2,000 bp were removed from each bin. phylosift () and jspeciesws () […]

2016
PMCID: 5054310
PMID: 27795237
DOI: 10.1128/genomeA.01024-16

[…] (version 3.7.0) (). the metagenome assembly yielded 12,264 total contigs (12,332,388 bp), with an n50 of 4,275 and a gc% of 56.52 (sra accession no. srp079849). the metagenome was binned with vizbin () and 22.5% of the contigs were assigned to the genus pseudomonas. the metagenome reads were mapped to the contigs of the pseudomonas genome bin using clc genomics workbench (qiagen) […]


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VizBin in publications

 (13)
PMCID: 5913679
PMID: 29554291
DOI: 10.1093/molbev/msy029

[…] of b. pusilla isolates kvj2, kvj10, kvj20, and kvs11 revealed some contamination with bacterial dna. thus, assemblies for these individual genomes were binned separately using t-sne ordination in vizbin () which identified cyanobacterial chromosome and plasmid assemblies as well as bacterial contaminants as separate bins. the genome characteristics of the symbiotic nostoc strains […]

PMCID: 5867873
PMID: 29518047
DOI: 10.3390/genes9030152

[…] was performed with metabat v0.26.3 []. checkm v1.0.5 [] was then used for assessment of completion and contamination of the extracted genomes or bins. further refinement of bins was carried out with vizbin v0.9 []. their taxonomic affiliation was determined by constructing a genomic tree with fasttree v2.1.3 [] of the concatenation of phylosift v.1.0.1 [] set of conserved genes […]

PMCID: 5834333
PMID: 29496841
DOI: 10.1128/genomeA.00140-18

[…] using megan v6.5.10 lowest common ancestor (lca) algorithm (), and extraction, refinement, and quality assessment of metagenome assembled genomes (mags) were accomplished with metabat v0.26.3 (), vizbin v0.9 (), and checkm v1.0.5. additionally, blastn searches of metagenomic reads of smo1 and smo2 against rdp database v11.4 () were performed to retrieve and classify 16s-related rrna reads., […]

PMCID: 5589535
PMID: 28883141
DOI: 10.1128/genomeA.00938-17

[…] from anaerobic mes enrichment cultures growing on 1,2-propanediol. illumina paired-end reads (56% desulfovibrio) were assembled with metaspades (default k-mer values), and contigs were binned with vizbin (). both genomes were manually curated for the removal of duplicate single-copy marker genes based upon checkm (version 1.0.7) output., the acetobacterium sp. strain mes1 draft genome consists […]

PMCID: 5356057
PMID: 28302780
DOI: 10.1128/genomeA.00033-17

[…] into contigs using clc-genomics-workbench version 8.5.1 (http://www.clcbio.com/products/clc-genomics-workbench) and spades version 3.5.1 (). assembled contigs were grouped into genome bins with vizbin () and taxonomy assessed with phylopythia (). metagenomic reads were mapped against binned contigs and reassembled using spades., the final draft genome contained 128 contigs of 5000 bp […]


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VizBin institution(s)
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Institute of Computing Science, Poznan University of Technology, Poznan, Poland; Computer Science and Communications Research Unit, University of Luxembourg, Luxembourg; Pattern Recognition and Bioinformatics Group, Delft University of Technology, CD Delft, Netherlands; Adobe Research, Adobe, San Jose, USA
VizBin funding source(s)
The present work was supported by an ATTRACT programme grant (A09/03) and a European Union Joint Programming in Neurodegenerative Diseases grant (INTER/JPND/12/01) and an Aide à la Formation Recherche grant (AFR PHD/4964712), all funded by the Luxembourg National Research Fund (FNR).

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