GroopM: an automated tool for the recovery of population genomes from related metagenomes.

PeerJ 2014 30;2:e603. Epub 2014 Sep 30.

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.

Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, and show that GroopM produces results comparable with more time consuming, labor-intensive methods.

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183954PMC
October 2014
45 Reads

Publication Analysis

Top Keywords

population genomes
8
genomes metagenomes
8
groopm automated
8
differential coverage
8
conventional composition-based
4
binning introduce
4
introduce groopm
4
composition-based binning
4
approach conventional
4
produces comparable
4
coverage emerging
4
emerging complementary
4
complementary approach
4
metagenomes groopm
4
groopm
4
groopm produces
4
tool differential
4
metagenomes demonstrate
4
groopm synthetic
4
demonstrate effectiveness
4

Altmetric Statistics

References

(Supplied by CrossRef)
CONCOCT: clustering cONtigs on COverage and ComposiTion
Alneberg et al.
2013
BLAST+: architecture and applications
Camacho et al.
BMC Bioinformatics 2009
Metagenomics: application of genomics to uncultured microorganisms
Handelsman et al.
Microbiology and Molecular Biology Reviews 2004
Exploring prokaryotic diversity in the genomic era
Hugenholtz et al.
Genome Biology 2002
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity
Hugenholtz et al.
Journal of Bacteriology 1998

Similar Publications