MetaWatt protocols

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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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  • person_outline mstrous <>

Publication for MetaWatt

MetaWatt in pipelines

 (9)
2018
PMCID: 5826079
PMID: 29515543
DOI: 10.3389/fmicb.2018.00260

[…] 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 […]

2017
PMCID: 5363838
PMID: 28094795
DOI: 10.1038/ismej.2016.175

[…] files loading, the ‘minimum overlap identity' was set to 99%, and ‘extend low depth overlaps' as well as ‘reads limited to one contig' were selected. contigs were binned using tetranucleotides with metawatt with its most relaxed settings, as previously described (). binning yielded four bins, representing three of the five abundant clades (for one of the clades, two bins were detected, see ). […]

2017
PMCID: 5519670
PMID: 28729646
DOI: 10.1038/s41598-017-05590-9

[…] reading frames (orfs). contigs with a minimum of 5x coverage were first separated into bacterial and archaeal bins via interpolated markov modeling, tetranucleotide binning, and blast performed in metawatt. orfs were detected using fraggenescan, and protein homologs were identified through blastp searches against the seed database (www.theseed.org). only hits to reference proteins […]

2017
PMCID: 5587575
PMID: 28878209
DOI: 10.1038/s41467-017-00342-9

[…] spades being specifically designed for assembly of single-cell data, no major differences in assembly were obtained when the normalized and raw data were used., the assembled data were binned using metawatt version 3.5.2. bins not associated to chromatiaceae were not used for further analysis. a similar binning approach was applied to four published genomes of achromatium , . metawatt was also […]

2017
PMCID: 5587575
PMID: 28878209
DOI: 10.1038/s41467-017-00342-9

[…] to achromatium were selected for single-cell genome sequencing. the sequencing was carried out as described above., single-cell genomes were assembled using spades (v 3.9) and binned using metawatt. genomic bins associated with chromatiaceae were extracted, the raw reads were mapped to the contained contigs and reassembled. the final scaffolds were annotated using prokka, rast, […]


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MetaWatt in publications

 (29)
PMCID: 5947290
PMID: 29468803
DOI: 10.1111/1462-2920.14077

[…] 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 […]

PMCID: 5826242
PMID: 29515540
DOI: 10.3389/fmicb.2018.00251

[…] ). 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 […]

PMCID: 5826079
PMID: 29515543
DOI: 10.3389/fmicb.2018.00260

[…] 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 […]

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

[…] 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 […]

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

[…] 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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