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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 citations

 (31)
library_books

Microbiome Dynamics in a Large Artificial Seawater Aquarium

2018
Appl Environ Microbiol
PMCID: 5930379
PMID: 29523545
DOI: 10.1128/AEM.00179-18

[…] genes involved in aerobic and anaerobic respiration, photosynthesis, and the oxidative stress response, and the resulting hits visualized to determine the contig position and transcription levels in anvi'o. The hits were also confirmed by their presence in the BLAST results. Putative plasmids were identified in anvi'o by the manual screening of gene annotations on contigs with aberrant GC content […]

library_books

Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen recycling gut microbiome

2018
Nat Commun
PMCID: 5840417
PMID: 29511180
DOI: 10.1038/s41467-018-03357-y

[…] To improve the assignment of metabolic capabilities to individual symbiont strains we used the Anvi’o metagenome visualization and annotation pipeline (version 1.2.3) in conjunction with the CONCOCT differential coverage-based binning program. In doing so, we binned a subset of assembled scaffo […]

library_books

A software tool ‘CroCo’ detects pervasive cross species contamination in next generation sequencing data

2018
BMC Biol
PMCID: 5838952
PMID: 29506533
DOI: 10.1186/s12915-018-0486-7

[…] verage and taxonomic assignment (using Basic Local Alignment Search Tool (BLAST) against the National Center for Biotechnology Information (NCBI) non-redundant database). A slightly different method, Anvi’o [], first automatically bins contigs based on read coverage and/or k-mer frequencies, then identifies the contaminant bins. Lastly, the algorithm Model-based Categorical Sequence Clustering (MC […]

library_books

Metaviz: interactive statistical and visual analysis of metagenomic data

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

[…] rovides 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 custom JavaScript visualizations (). MicrobiomeDB is a web service that hosts microbiome community taxonomic profile data from open dataset […]

library_books

Genome resolved metagenomics of sugarcane vinasse bacteria

2018
Biotechnol Biofuels
PMCID: 5822648
PMID: 29483941
DOI: 10.1186/s13068-018-1036-9

[…] st of each. Further, we used large kmer sizes for the final cross-assembly, and this successfully allowed MaxBin2 to bin to the level of species. We additionally used the manual refinement feature of anvi’o to improve the bins. Because bins with low completeness as determined by the presence of universal marker genes can still contain useful information regarding potential gene content, we used al […]

library_books

Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Species Strains from a Freshwater Ecosystem

2018
Genome Announc
PMCID: 5794932
PMID: 29437085
DOI: 10.1128/genomeA.00009-18

[…] ,000 bp with a total size of 74 Mbp. From this metagenomic assembly, three genomes belonging to the Pseudomonas, Flavobacterium, and Sediminibacterium genera were binned using the manually supervised anvi’o protocol based on the abundance and tetranucleotide frequency distributions () and quality controlled by CheckM () (100%, 99%, and 99% predicted completeness, respectively, with an indication o […]

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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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