MetaBAT protocols

View MetaBAT computational protocol

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MetaBAT specifications

Information


Unique identifier OMICS_10415
Name MetaBAT
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data MetaBAT takes an assembly file (fasta format, required) and sorted bam files (one per sample, optional) as inputs.
Output data Each discovered bin will be saved as a fasta format.
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Requirements
Boost, Python, scons, g++, zlib
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Zhong Wang <>

Publication for MetaBAT

MetaBAT in pipelines

 (9)
2018
PMCID: 5826242
PMID: 29515540
DOI: 10.3389/fmicb.2018.00251

[…] (default parameters) (li et al., ). the reads from each sample were mapped back to these assembled contigs using bbmap (https://sourceforge.net/projects/bbmap/) and then all data was binned using metabat (kang et al., ) to generate the draft genomes. the completeness and taxonomical classification were checked using checkm (parks et al., )., dna fasta files of the generated bins (288) […]

2017
PMCID: 5552984
PMID: 28798175
DOI: 10.1128/genomeA.00763-17

[…] up to 99 bp. scaffolds of this preassembly ≥500 bp were subject to extension and second-round scaffolding with sspace standard version 3.0 (). scaffolds ≥2,500 bp were assigned to genome bins by metabat version 0.32.4 (), and functional annotation of draft genomes was performed with prokka version 1.12b (). the shortest scaffold was 2,712 bp, and the longest scaffold was 335,770 bp. […]

2017
PMCID: 5636890
PMID: 29021524
DOI: 10.1038/s41467-017-01086-2

[…] are publicly available in the jgi’s integrated microbial genome database with genome id’s 3300000439, 3300000553, and 3300002835, respectively., assembled contigs were grouped into genome bins using metabat (–veryspecific settings, minimum bin size of 20 kb, minimum contig size of 2.5 kb). for this binning, coverage levels were determined from metagenomic reads mapping with ≥ 95% sequence […]

2017
PMCID: 5691036
PMID: 29146959
DOI: 10.1038/s41467-017-01753-4

[…] proteins, with only a prediction from prodigal but a bit score < 60., assembled scaffolds were binned into genomes based on gc, coverage, and taxonomic affiliation across samples using esom and metabat. for each bin, genome completion was estimated based on the presence of core gene sets (highly conserved genes that occur in single copy) for bacteria (31 genes) and archaea (104 genes) using […]

2017
PMCID: 5727513
PMID: 29235508
DOI: 10.1038/s41598-017-17640-3

[…] samples were pooled together and assembled using megahit (version 1.1) with k-mer size from 27 to 99 with a step of 10. contigs with a length over 2.5 kbp were organized into genome bins (gbs) using metabat (version 0.32.4) based on the tetranucleotide sequence composition and overall contig coverage patterns obtained from backtrack alignment files. reads from each sample were mapped […]


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MetaBAT in publications

 (55)
PMCID: 5897806
PMID: 29650584
DOI: 10.1128/genomeA.00325-18

[…] up to 99 bp. scaffolds ≥500 bp of this preassembly were subject to extension and second-round scaffolding with the sspace standard version 3.0 (). scaffolds ≥2,500 bp were assigned to genome bins by metabat version 0.32.4 (), and functional annotation of the draft genomes was performed with prokka version 1.12b ()., the draft genome included 73 contigs, with an n50 assembly quality of 107,389 bp […]

PMCID: 5897805
PMID: 29650587
DOI: 10.1128/genomeA.00335-18

[…] up to 99 bp. scaffolds of ≥500 bp of this preassembly were subject to extension and second-round scaffolding with sspace standard v3.0 (). scaffolds of ≥2,500 bp were assigned to genome bins by metabat v0.32.4 (), and functional annotation of the draft genomes was performed with prokka v1.12b (). the draft genome included 270 scaffolds with an n50 assembly quality of 39,507 and an l50 value […]

PMCID: 5955933
PMID: 29581530
DOI: 10.1038/s41396-018-0098-9

[…] bases, and were assembled using metaspades [] with the following parameters (--only-assembler -k 31,41,51,61,71,81,91,101,111,121). assembled scaffolds ≥ 2500 bp were binned separately using metabat v0.26.1 [] and mycc []. results of two binning methods for each sample were combined and a non-redundant set of bins was chosen. the acquired genomes were curated manually with two […]

PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] another possible option for compositional analysis, which we did not explore here, is to use a de novo metagenome assembly approach, wherein genomes are binned using tools like concoct [] or metabat [], and reads are then mapped against these bins to calculate species abundances. an advantage of such an approach is that it does not rely on a reference database for diversity analysis […]

PMCID: 5867873
PMID: 29518047
DOI: 10.3390/genes9030152

[…] manually curated. functional annotation of reads and contigs was carried out using cognizer v0.9b []. rarefaction curves were computed with qiime pipeline v1.9.1 []. , binning was performed with metabat v0.26.3 []. checkm v1.0.5 [] was then used for assessment of completion and contamination of the extracted genomes or bins. further refinement of bins was carried out with vizbin v0.9 []. […]


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MetaBAT institution(s)
Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; School of Natural Sciences, University of California at Merced, Merced, CA, USA
MetaBAT funding source(s)
The work was supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231.

MetaBAT review

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Sarah Turner

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Desktop
I think this is a useful and easy-to-use tool. However, it did not perform well with samples containing a large number of unknown/unidentified organisms (freshwater sediment), and may be more useful in situations where more of the taxa present in a sample have references available.