CONCOCT pipeline

CONCOCT specifications


Unique identifier OMICS_06387
Alternative name Clustering cONtigs with COverage and ComposiTion
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes



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Publication for Clustering cONtigs with COverage and ComposiTion

CONCOCT IN pipelines

PMCID: 5754496
PMID: 29301887
DOI: 10.1128/genomeA.01416-17

[…] samples were pre-processed using bbtools (6) and coassembled using metaspades (7). contigs were taxonomically assigned using kaiju (8) and binned on the basis of gc% and differential coverage using concoct (9)., the resulting bins were manually refined to reduce contamination using anvi’o (10); briefly, for each bin, contigs were clustered on the basis of gc% by euclidean distance and ward’s […]

PMCID: 4863621
PMID: 27303675
DOI: 10.1128/mSphere.00054-15

[…] (hao). this metagenome bin was discovered through shotgun dna sequencing of samples from biologically active filters at a drinking water treatment plant (ann arbor, mi). idba-ud assembly (7), concoct genome binning (8), and manual curation (see text s1 in the supplemental material) resulted in 51 high-quality draft genomes with 2 to 755 scaffolds (median = 73), n50 ranging from 7.4 to 114 […]

CONCOCT institution(s)
KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden; Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm, Sweden; School of Engineering, University of Glasgow, Glasgow, UK; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK; National Institute for Health Research Surgical Reconstruction (NIHR) Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, UK; Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland; Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands

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