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GroopM specifications

Information


Unique identifier OMICS_08844
Name GroopM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.3.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Gene W. Tyson

Publication for GroopM

GroopM citations

 (18)
library_books

Metabolic capability and in situ activity of microorganisms in an oil reservoir

2018
Microbiome
PMCID: 5756336
PMID: 29304850
DOI: 10.1186/s40168-017-0392-1

[…] Co-assembled contigs were used for differential binning []. In brief, individual trimmed reads were mapped back to the contigs file, and the resulting bam files were used as input into GroopM with default parameters (v0.3.4) []. De-contamination of retrieved genome bins (GBs) was carried out in ProDeGe []. Bonafide GBs were uploaded to RAST [] for annotation. All GBs were checked fo […]

library_books

Optimizing and evaluating the reconstruction of Metagenome assembled microbial genomes

2017
BMC Genomics
PMCID: 5706307
PMID: 29183281
DOI: 10.1186/s12864-017-4294-1

[…] binning tool because the bins had minimal GC variation, species richness, and high genome completeness that may represent a single genome. The number of bins extracted by MetaBat was low compared to GroopM extracted bins. MetaBat bins were further validated using taxonomic identification to show the workflow reconstructed 66 metagenome-assembled genomes. These metagenome-assembled genomes include […]

library_books

Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico

2017
Sci Rep
PMCID: 5700182
PMID: 29167487
DOI: 10.1038/s41598-017-16375-5

[…] m outside the seep area. Shotgun metagenome sequencing was carried out on 6 sediment samples (3–4 and 10–12 cmbsf sediment layers from PC5, PC10 and PC12). Despite numerous attempts using Metabat and GroopM, metagenomic binning of draft genomes was unsuccessful. This is probably due to high variability of the sequences coupled to limited sequencing depth, which make assembly challenging. Therefore […]

library_books

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton

2017
PMCID: 5739002
PMID: 28895945
DOI: 10.1038/ismej.2017.142

[…] using the ‘meta-sensitive’ option and kmer length of 81. Metagenome binning was done based on differential coverage and tetranucleotide signatures for each assembly separately using the binning tools GroopM v0.3.4 () and Metabat v0.25.4 (). Genome contamination and completeness were assessed using CheckM v1.0.3 (). To increase genome completeness, the ‘merge’ option from CheckM was used and popula […]

library_books

Methane Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea

2017
MBio
PMCID: 5539420
PMID: 28765215
DOI: 10.1128/mBio.00530-17

[…] ibed previously (). Briefly, these samples were sequenced using a HiSeq 2000 system (Illumina, Inc., San Diego, CA) and assembled using CLC genomics workbench 6.0; metagenomic bins were defined using GroopM 0.2 (). Additionally, a second assembly procedure was performed on the samples using megahit 0.3.3a (), and the results were then binned using metabat 0.26.1 (). This assembly and binning compl […]

library_books

Relative abundance of ‘Candidatus Tenderia electrophaga’ is linked to cathodic current in an aerobic biocathode community

2017
PMCID: 5743799
PMID: 28696003
DOI: 10.1111/1751-7915.12757

[…] m. Three settings were assessed for metabat: sensitive (metabat 1), super‐sensitive (metabat 2) and super‐specific (metabat 3). Only default or easily implemented optional settings were tested. While groopm and metabat both have many parameters that can be adjusted only metabat provides batch choice settings that set all the parameters at the time of this manuscript preparation. AMPHORA2 was used […]

Citations

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GroopM institution(s)
Australian Center for Ecogenomics (ACE), School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia; Advanced Water Management Center (AWMC), The University of Queensland, St Lucia, QLD, Australia

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