MetaWatt statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MetaWatt
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Tool usage distribution map

This map represents all the scientific publications referring to MetaWatt per scientific context
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Protocols

MetaWatt specifications

Information


Unique identifier OMICS_07552
Name MetaWatt
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Assembled contigs, shotgun reads
Output data Provisional whole genome sequences (bins)
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux, Mac OS
Programming languages Java
Computer skills Advanced
Version 3.1
Stability Stable
Requirements
DIAMOND, prodigal, aragorn, bbmap, hmmer
Maintained Yes

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Maintainer


  • person_outline mstrous

Publication for MetaWatt

MetaWatt citations

 (31)
library_books

Gene expression and ultrastructure of meso‐ and thermophilic methanotrophic consortia

2018
Environ Microbiol
PMCID: 5947290
PMID: 29468803
DOI: 10.1111/1462-2920.14077

[…] nformation. In short, raw reads were quality controlled using BBDuk (v35.14) (https://sourceforge.net/projects/bbmap/), assembled with SPAdes v3.5.0 (Bankevich et al., ) and contigs binned within the Metawatt software v3.2 (Strous et al., ). Bins of contigs identified as ANME or partner bacterium were extracted from the bulk assembly for targeted reassembly with SPAdes. Assembly quality and bin co […]

library_books

Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome Resolved Metagenomics

2018
Front Microbiol
PMCID: 5826242
PMID: 29515540
DOI: 10.3389/fmicb.2018.00251

[…] löckner, ). Recently, some new algorithms have been proposed to overcome these limitations and to obtain partial or near complete genomes from environmental samples, e.g., MetaBat (Kang et al., ) and MetaWatt (Strous et al., ). Most of them require many samples and high coverage sequencing per sample as an input. Recently, studies have been done to recover genomes even from rare bacteria (Albertse […]

library_books

Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer

2018
Front Microbiol
PMCID: 5826079
PMID: 29515543
DOI: 10.3389/fmicb.2018.00260

[…] bp paired-end sequencing via Illumina HiSeq 4,000 technology. Raw sequence reads were assembled with MegaHit v. 1.02 (Li et al., ) and genome bins constructed based on tetranucleotide frequency using MetaWatt version 3.5.2 (Strous et al., ). Genomes were manually screened for genes of interest and uploaded to RAST (Aziz et al., ) for overall characterization. Genome bins were assessed for complete […]

library_books

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision

2017
BMC Bioinformatics
PMCID: 5751405
PMID: 29297295
DOI: 10.1186/s12859-017-1967-3

[…] strategies were evaluated on their recall in binning datasets of different complexities (in Additional file : Table S1). Both MaxBin and MyCC (coverage) had the highest ranking score in recall, while Metawatt had the lowest ranking score in recall. CoMet had a lower ranking score than MaxBin, MyCC (coverage) and MyCC (default), but yielded higher or comparable recall values in comparison to Metawa […]

library_books

Genomic features of “Candidatus Venteria ishoeyi”, a new sulfur oxidizing macrobacterium from the Humboldt Sulfuretum off Chile

2017
PLoS One
PMCID: 5728499
PMID: 29236755
DOI: 10.1371/journal.pone.0188371

[…] by a custom python script and scaffolds >1000 bp were selected for gene prediction.In order to determine possible contamination, the draft genome obtained was subjected to binning analysis using the MetaWatt software []. Moreover, the Amphora2 software [] was used to evaluate the presence of 32 bacterial marker genes. The genome completeness of “Ca. V. ishoeyi” was assessed using the number of id […]

library_books

Assessing species biomass contributions in microbial communities via metaproteomics

2017
Nat Commun
PMCID: 5691128
PMID: 29146960
DOI: 10.1038/s41467-017-01544-x

[…] r the uneven samples were concatenated and assembled with metaSPAdes (version 3.8.1). The assembly quality was checked by running metaQUAST (version 4.1) with the mock community reference genome set. Metawatt (version 3.5.2) was then used to create bins for AK199 and C. violaceum CV026 using default settings. The bins were checked with metaQUAST to ensure that none of the included contigs aligned […]


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MetaWatt institution(s)
University of Calgary, Canada

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