Anvi'o protocols

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Anvi'o specifications

Information


Unique identifier OMICS_15467
Name Anvi'o
Alternative name analysis and visualization platform for 'omics data
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Javascript, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.1.0
Stability Stable
Requirements
Numpy, cython, bottle, pysam, ete2, Scipy, SciKit-learn, Django, h5py, cherrypie, requests
Maintained Yes

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Maintainer


  • person_outline Murat Eren <>

Publication for analysis and visualization platform for 'omics data

Anvi'o in pipelines

 (4)
2018
PMCID: 5930379
PMID: 29523545
DOI: 10.1128/AEM.00179-18

[…] from each sample and the coassembled metagenome (2,500-bp assembly), using maxbin 2.0 (). the recruitment of short reads to each mag was calculated by using bowtie2. metagenomes were imported into anvi'o v2.4.0 () for alignment, visualization, and manual refinement, including the removal of contigs containing eukaryotic rrnas and plasmids. refined mags were analyzed for completeness […]

2017
PMCID: 5394123
PMID: 28458657
DOI: 10.3389/fmicb.2017.00618

[…] barrier reef (sato et al., ), a roseofilum culture from the great barrier reef (buerger et al., ), and a geitlerinema culture from caribbean black band mat (den uyl et al., ) was performed with anvi'o v.2.1.0, in which proteins were clustered with the mcl algorithm (van dongen and abreu-goodger, ) using 2 for the mcl inflation parameter and identified by ncbi's blastp (altschul et al., )., […]

2017
PMCID: 5671498
PMID: 29164068
DOI: 10.3389/fcimb.2017.00459

[…] genes as a function of the number of strains (knight et al., )., both the core- and pan-genomes were visualized through pangp (zhao et al., ), qtiplot v0.9.9.11 (http://www.qtiplot.com/), and anvi'o (eren et al., ), using the above-mentioned binary matrix as an input., all protein sequences were aligned using blastp (altschul et al., ) against the virulence factor database for bacterial […]

2015
PMCID: 4620155
PMID: 26579075
DOI: 10.3389/fmicb.2015.01090

[…] were clustered with the bacterial scaffolds due to a more similar evolutionary origin, douglas, ). note that our metagenomic assembly visualization and binning approaches can be performed using the anvi'o platform (eren et al., )., we used rast (aziz et al., ) and figfam (meyer et al., ) version 64 to annotate our scaffolds. we then compared our draft genomes to available genomes at the protein […]


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Anvi'o in publications

 (7)
PMCID: 5930379
PMID: 29523545
DOI: 10.1128/AEM.00179-18

[…] sample 0928 reads generated 6 mags, 3 of which were nearly complete (>96.8%) (table s5). four eukaryotic rrna sequences were identified, and the associated contigs were removed from the mags with anvi'o (table s8). bacterial rrna genes were detected in only 5 of the 16 total mags, and in one case (mag 0928_002), they were likely spuriously binned, as judged by comparison to the mag taxonomic […]

PMCID: 5671498
PMID: 29164068
DOI: 10.3389/fcimb.2017.00459

[…] genes as a function of the number of strains (knight et al., )., both the core- and pan-genomes were visualized through pangp (zhao et al., ), qtiplot v0.9.9.11 (http://www.qtiplot.com/), and anvi'o (eren et al., ), using the above-mentioned binary matrix as an input., all protein sequences were aligned using blastp (altschul et al., ) against the virulence factor database for bacterial […]

PMCID: 5635047
PMID: 29056932
DOI: 10.3389/fmicb.2017.01933

[…] deviations owing to the different annotation processes, the re-annotation of all the genomes were performed by prokka version 1.12 (seemann, ). visualization of the pan-genome data was performed by anvi'o (eren et al., )., the results from the infection of tilapia with 10 isolates of human st23 gbs were shown in figure . the lowest mortality rate was 76.67% and the highest mortality rate […]

PMCID: 5394123
PMID: 28458657
DOI: 10.3389/fmicb.2017.00618

[…] removed from the bin. summary statistics for each mag were determined with quast v. 2.3 (gurevich et al., ). genome completeness and the presence of contamination within mags was determined with anvi'o v. 2.1.0 (eren et al., ), using four different sets of single-copy genes. antibiotic and secondary metabolite biosynthetic genes in mags were identified using antismash v. 3.0 (weber et al., […]

PMCID: 5286201
PMID: 28117401
DOI: 10.1038/ncomms14061

[…] at: https://figshare.com/projects/fission_yeast_structural_variation/15798., circle plots were used to visualize the variation in copy number over the snp-based phylogeny for each cnv using anvi'o (version 2.0.3)., sequence data are archived in the european nucleotide archive under study accessions prjeb2733 and prjeb6284. snp, indel and svs calls, genotypes and copy numbers […]


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Anvi'o institution(s)
Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA; Department of Medicine, The University of Chicago, Chicago, IL, USA; Warwick Medical School, University of Warwick, Coventry, UK
Anvi'o funding source(s)
This work was supported by the G. Unger Vetlesen Foundation, and the Frank R. Lillie Research Innovation Award given by the University of Chicago and the Marine Biological Laboratory.

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