MetaVelvet statistics

info info

Citations per year

info

Popular tool citations

chevron_left Assembly chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

Protocols

MetaVelvet specifications

Information


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
Requirements
zlib, velveth, velvetg, g++
Maintained Yes

Download


galaxy.png
conda.png

Versioning


No version available

Maintainer


  • person_outline Yasubumi Sakakibara

Publication for MetaVelvet

MetaVelvet citations

 (76)
library_books

Studying microbial functionality within the gut ecosystem by systems biology

2018
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 […]

library_books

Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

2018
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 […]

library_books

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

2017
Proteomes
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, […]

library_books

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

2017
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 […]

library_books

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

2017
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 […]

library_books

Optimizing and evaluating the reconstruction of Metagenome assembled microbial genomes

2017
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 […]


Want to access the full list of citations?
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).

MetaVelvet reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MetaVelvet