MetaBAT pipeline

MetaBAT specifications


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


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  • person_outline Zhong Wang <>

Publication for MetaBAT

MetaBAT IN pipeline

PMCID: 5663940
PMID: 29104938
DOI: 10.1128/mSystems.00038-17

[…] the reads back to the scaffolds using bbmap (b. bushnell;, and for computing coverage, bedtools (version 2.18.2) (58) was used. scaffolds were binned using metabat (59), and the criteria for high-quality bins (corresponding to the so-called mags) were based on checkm (60) estimates of completeness (>70%) and contamination (<5%)., in addition […]

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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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.