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MetaVelvet specifications


Unique identifier OMICS_01427
Name MetaVelvet
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A set of the nucleotide sequences of DNA fragments.
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.01
Stability Stable
zlib, velveth, velvetg, g++
Maintained Yes




No version available


  • person_outline Yasubumi Sakakibara

Publication for MetaVelvet

MetaVelvet citations


Studying microbial functionality within the gut ecosystem by systems biology

PMCID: 5840735
PMID: 29556373
DOI: 10.1186/s12263-018-0594-6

[…] evenness need to be taken into account to evaluate if the mapping rate is appropriate for further analysis., some of these challenges have been tackled with specific metagenome assemblers like metavelvet [], which take different properties of the sequencing data into account like for example the different abundances of the potentially present species. currently, a community-derived […]


Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

Int J Mol Sci
PMCID: 5855605
PMID: 29382070
DOI: 10.3390/ijms19020383

[…] of different genomes that are present in different proportions within the studied community., specific assemblers have been developed for shotgun metagenomics (), such as soapdenovo [], velvet [], metavelvet [], meta-ibda [], genovo [], bambus2 [], and ray-meta []. currently, there is no unique consensus regarding the best assembly strategy, since it has been noticed that the assembler […]


Multi Omic Biogeography of the Gastrointestinal Microbiota of a Pre Weaned Lamb

PMCID: 5748571
PMID: 29258228
DOI: 10.3390/proteomes5040036

[…] paired reads were merged, filtered and clustered using usearch (version 8.0.1623) [], with previously illustrated parameters []. in parallel, raw reads were also assembled into contigs using metavelvet (version 1.2.01) [], with 61 as k-mer length, 200 as insert length and 300 as minimum contig length. finally, fraggenescan (version 1.30) [] was used to find open reading frames, […]


Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

Proc Natl Acad Sci U S A
PMCID: 5776962
PMID: 29255014
DOI: 10.1073/pnas.1708779115

[…] using a standard phenol extraction protocol (). contigs were assembled using paired-end illumina hiseq reads, and the assembly and prediction of orfs were performed using the software tools metavelvet and prokka (). 16s rrna gene sequences were assembled using emirge () and identified by blastn searching against the silva ssu 128 database ()., protein extraction and spin filter-aided […]


Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium

Front Microbiol
PMCID: 5735121
PMID: 29312205
DOI: 10.3389/fmicb.2017.02499

[…] emg taxonomic and functional profiling of unassembled reads, we performed cog-based annotations of both unassembled and assembled reads on mg-rast. assembly of metagenomes was carried out using metavelvet () with default parameters. thereafter, assembled and unassembled data were processed within mg-rast as described above. predicted protein sequences were searched against the cog database […]


Optimizing and evaluating the reconstruction of Metagenome assembled microbial genomes

BMC Genomics
PMCID: 5706307
PMID: 29183281
DOI: 10.1186/s12864-017-4294-1

[…] the assembly and binning processes on population genome reconstruction using 105 marine metagenomes from 4 projects. reconstructed genomes were obtained from each project using 3 assemblers (idba, metavelvet, and spades) and 2 binning tools (groopm and metabat). we assessed the efficiency of assemblers using statistics that including contig continuity and contig chimerism and the effectiveness […]

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MetaVelvet institution(s)
Department of Biosciences and Informatics, Keio University, Yokohama, Japan; Japan Post Network Co., Tokyo, Japan
MetaVelvet funding source(s)
Supported by KAKENHI from the Ministry of Education, Culture, Sports, Science and Technology of Japan [Grant-in-Aid for Scientific Research on Innovative Areas No.221S0002] and a grant program for bioinformatics research and development of the Japan Science and Technology Agency (in part).

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