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Deblur specifications

Information


Unique identifier OMICS_16645
Name Deblur
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Rob Knight

Publication for Deblur

Deblur citations

 (47)
library_books

Microbiome Dynamics in a Large Artificial Seawater Aquarium

2018
Appl Environ Microbiol
PMCID: 5930379
PMID: 29523545
DOI: 10.1128/AEM.00179-18

[…] a minimum length cutoff of 150 bases. the hots data were downloaded from the sra as quality-filtered reads. forward-paired reads from all data sets were merged into one fasta file and run through deblur () (cutoff length of 150 bp) and qiime v1.9.1 () to assess community composition. the use of deblur meant that sequences were not clustered into operational taxonomic units but rather […]

library_books

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

2018
mSystems
PMCID: 5904434
PMID: 29719869
DOI: 10.1128/mSystems.00021-18

[…] have enabled the derivation of exact amplicon sequence fragments. instead of the coarse operational taxonomic units (otus) that have dominated the field for over a decade, these new methods (e.g., deblur [] and dada2 []) enable the investigation of sub-otus (sotus) through the removal of erroneous sequences and add the ability to analyze amplicon data at maximal resolution. however, […]

library_books

Fast first photon ghost imaging

2018
Sci Rep
PMCID: 5864734
PMID: 29567969
DOI: 10.1038/s41598-018-23363-w

[…] is designing a better measurement system,. for the former, many approaches based on wavelet-based methods,, were proposed. later, more general and effective sparsity models have been investigated to deblur the poisson noise, such as total variation, logarithmic regularization,, and the models based on image patches,. kirmani et al. proposed a first-photon imaging(fpi) technique, which recovers […]

library_books

KatharoSeq Enables High Throughput Microbiome Analysis from Low Biomass Samples

2018
mSystems
PMCID: 5864415
PMID: 29577086
DOI: 10.1128/mSystems.00218-17

[…] unique microbiomes reproducible across hundreds of samples. the saf, our primary focus, contains 32 sotus (sub-otus, defined as exact sequence matches) and their inferred variants identified by the deblur algorithm, with four (acinetobacter lwoffii, paracoccus marcusii, mycobacterium sp., and novosphingobium) being present in >75% of the samples. according to microbial spatial topography, […]

library_books

Deblurring traffic sign images based on exemplars

2018
PLoS One
PMCID: 5841653
PMID: 29513677
DOI: 10.1371/journal.pone.0191367

[…] authors have declared that no competing interests exist., motion blur appearing in traffic sign images may lead to poor recognition results, and therefore it is of great significance to study how to deblur the images. in this paper, a novel method for deblurring traffic sign is proposed based on exemplars and several related approaches are also made. first, an exemplar dataset construction […]

library_books

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models

2018
Genes
PMCID: 5852600
PMID: 29462950
DOI: 10.3390/genes9020104

[…] available and curated on qiita where they are periodically re-annotated to be consistent with current best practices utilizing the qiime pipeline [,]. therefore, we utilized data processed using the deblur method, which utilizes sequence error profiles to derive putatively true biological sequences, resulting in high quality sequence variant data as opposed to operational taxonomic units (otus) […]


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Deblur institution(s)
Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Applied Mathematics, and Interdisciplinary Quantitative Biology Graduate Program, University of Colorado Boulder, Boulder, CO, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
Deblur funding source(s)
Supported by the Sloan Foundation, the National Science Foundation (grants DBI-1565057 and DGE-1144086), the Department of Defense (grants W81XWH- 15-1-0653 and N0001-14-15-1-2809), and the National Institutes of Health (grant P01DK078669).

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