MetaVelvet protocols

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MetaVelvet specifications

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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

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Maintainer


  • person_outline Yasubumi Sakakibara <>

Publication for MetaVelvet

MetaVelvet in pipelines

 (5)
2017
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 […]

2016
PMCID: 4802719
PMID: 27001503
DOI: 10.1186/s12866-016-0669-8

[…] size of 300 bp. all the outsourcing for dna sequencing was done at xcelris lab pvt ltd, ahmedabad, india., sequences generated for polluted as well as control sample was assembled individually by metavelvet assembler (1.20.02) [, ] set at k = 31, −exp cov = auto, −cov_cutoff = auto and insertion length with standard deviation = 300 bp ± 20. both raw reads and contigs were used […]

2016
PMCID: 4940381
PMID: 27462302
DOI: 10.3389/fmicb.2016.01058

[…] sequence were considered., reads from a total of 38 individual gm metagenomes, 27 hadza and 11 italians from , were downloaded and included in this study. reads were assembled into contigs using metavelvet () with 350 bp as insert length. predicted open reading frames (orfs) were determined by fraggenescan () on assembled contigs, using the “–w 0” option for the fragmented genomic sequences […]

2014
PMCID: 4044621
PMID: 24894641
DOI: 10.1038/srep05113

[…] contigs were ordered according to reference sequences (py. yezoensis, py. haitanensis, and po. purpurea). to validate the joined contigs, targeted pcr and sequencing, and assembly comparisons to metavelvet contig results, were analyzed on the first three genomes assembled (ld-ag 13037, uc 807662, vk-11-00061). genomes processed later were confirmed by aligning sequence reads against a draft […]

2014
PMCID: 4226467
PMID: 25383623
DOI: 10.1371/journal.pone.0110505

[…] blastp hits per 10 million input sequences (±sd). the minimum % identity cutoff was 70%; the minimum alignment length was 21 amino acids., a de novo assembly of processed sequence reads using metavelvet resulted in 142,061 contigs with a mean n50 = 715 bp (±337.32; sd) per sample. approximately 175,375 orfs were predicted from these contigs using fraggenescan. the orfs were annotated […]


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MetaVelvet in publications

 (76)
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 […]

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 […]

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, […]

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 […]

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 […]


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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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