microbeGPS specifications


Unique identifier OMICS_17085
Name microbeGPS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Bernhard Renard <>

Publication for microbeGPS

microbeGPS in publications

PMCID: 5751639
PMID: 29297282
DOI: 10.1186/s12859-017-1901-8

[…] objective of metagenomics analysis focuses on profiling known bacteria, it is complicated by the presence of unknown bacteria (or those without sequenced genomes). to the best of our knowledge, only microbegps [] provides a basic analysis of unknown bacteria in how they are similar to known bacteria. it does not address the scenario where unknown bacterial genomes are vastly different […]

PMCID: 5600177
PMID: 28924496
DOI: 10.7717/peerj.3729

[…] are not robust to horizontal gene transfer events and therefore alternative classification algorithms may be more suitable for contaminant detection than pathoscope (; ). other methods such as microbegps and dudes are alternative similarity based taxonomic classification methods developed to better handle organisms not in a reference database and are also suitable alternatives […]

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microbeGPS institution(s)
ResearchGroupBioinformatics(NG4), RobertKochInstitute, Berlin, Germany
microbeGPS funding source(s)
Supported by the German Federal Ministry of Health [IIA5-2512-FSB-725].

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