DBC statistics

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Citations per year

Number of citations per year for the bioinformatics software tool DBC
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Tool usage distribution map

This map represents all the scientific publications referring to DBC per scientific context
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Associated diseases

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Protocols

DBC specifications

Information


Unique identifier OMICS_23381
Name DBC
Alternative name Distribution-based clustering
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Shell (Bash)
Computer skills Advanced
Stability Stable
Requirements
QIIME, USEARCH, mothur, FastTree, uchime
Maintained Yes

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Maintainer


  • person_outline Eric Alm

Publication for Distribution-based clustering

DBC citations

 (10)
call_split

High resolution time series reveals cohesive but short lived communities in coastal plankton

2018
Nat Commun
PMCID: 5773528
PMID: 29348571
DOI: 10.1038/s41467-017-02571-4
call_split See protocol

[…] To identify populations at high taxonomic resolution, we used the distribution-based clustering algorithm to group rRNA gene sequences into OTUs. This approach takes into account both genetic distance and the distribution of sequences across samples. Specifically, i […]

call_split

Ecological selection of siderophore‐producing microbial taxa in response to heavy metal contamination

2017
Ecol Lett
PMCID: 5765521
PMID: 29161760
DOI: 10.1111/ele.12878
call_split See protocol

[…] ocessed using default parameters of the SmileTrain pipeline (https://github.com/almlab/SmileTrain/wiki/), including reads quality and chimera filtering, paired‐end joining, de‐replication and de novo distribution‐based clustering using USEARCH (Edgar ; http://www.drive5.com/usearch), Mothur (Schloss et al. ), Biopython, dbOTUcaller algorithms (Preheim et al. ; https://github.com/spacocha/dbOTUcall […]

call_split

The Inuit gut microbiome is dynamic over time and shaped by traditional foods

2017
Microbiome
PMCID: 5689144
PMID: 29145891
DOI: 10.1186/s40168-017-0370-7
call_split See protocol

[…] f raw sequences, and postclustering dereplication were performed on raw sequences using USEARCH v. 7.0.1090 []. Operational taxonomic units (OTUs) were called from the filtered reads, using a de novo distribution-based clustering method, with otu_caller.py script from SmileTrain which performs a custom algorithm using USEARCH. This clustering method takes into account the distribution of DNA seque […]

call_split

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white nose syndrome

2017
Microbiome
PMCID: 5584028
PMID: 28870257
DOI: 10.1186/s40168-017-0334-y
call_split See protocol

[…] ring, quality filtering, primer removal, merging of raw sequences, and postclustering dereplication were performed with the SmileTrain scripts [] for 16S data processing using USEARCH v. 7.0.1090 []. Distribution-based clustering using the dbOTUcaller algorithm was performed to cluster sequences into OTUs by considering the distribution of DNA sequences across samples and distances between sequenc […]

library_books

Reconciliation between operational taxonomic units and species boundaries

2017
PMCID: 5812548
PMID: 28334218
DOI: 10.1093/femsec/fix029

[…] threshold, advanced algorithms have been developed resolving fine-scale variation without inflating the amount of OTUs caused by sequencing errors, e.g. DADA2 (Callahan et al.), Swarm (Mahé et al.), distribution-based clustering (Preheim et al.), MED (Eren et al.) and CROP (Hao, Jiang and Chen ).Although the current definition of a bacterial species has been a matter of debate for many decades (H […]

call_split

Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor

2017
PLoS One
PMCID: 5308813
PMID: 28196102
DOI: 10.1371/journal.pone.0171369
call_split See protocol

[…] east 99 bps long after quality filtering was retained. After quality-filtering, 16S rRNA universal primer sequences were removed from all reads, Operational Taxonomic Units (OTUs) were assigned using distribution-based clustering with default parameters, and singletons were removed using methods described in Preheim, et al. [] (). […]


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DBC institution(s)
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
DBC funding source(s)
Supported by the Office of Science, Office of Biological and Environmental Research, of the U.S. Department of Energy under contract no. DE- AC02-05CH11231.

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