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RDPipeline specifications

Information


Unique identifier OMICS_02158
Name RDPipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Roche
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Information


Unique identifier OMICS_02158
Name RDPipeline
Interface Web user interface
Restrictions to use None
Biological technology Roche
Computer skills Basic
Stability Stable
Maintained Yes

RDPipeline citations

 (9)
library_books

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

2018
Appl Environ Microbiol
PMCID: 5861821
PMID: 29427429
DOI: 10.1128/AEM.02627-17

[…] predominantly in their accessibility to those with limited computational knowledge and in the availability of documentation.Nilakanta et al. compared seven different packages (mothur, QIIME, WATERS, RDPipeline, VAMPS, Genboree, and SnoWMan) and concluded that while all of these packages provide effective pipelines for 16S rRNA gene analysis, the extensive documentation which accompanies mothur an […]

call_split

Effects of cosmetics on the skin microbiome of facial cheeks with different hydration levels

2017
PMCID: 5911989
PMID: 29193830
DOI: 10.1002/mbo3.557
call_split See protocol

[…] d read lengths longer than 300 nucleotides were selected for further analysis. Potential chimeric sequences were removed using UCHIME Chimera Slayer (Edgar, Haas, Clemente, Quince, & Knight, ) in the RDPipeline, and nonbacterial reads including chloroplast, mitochondrial, archaeal, and eukaryotic sequences were also discarded by the remove.lineage command within the Mothur program (Schloss et al., […]

call_split

Suppression of Fusarium wilt of cucumber by ammonia gas fumigation via reduction of Fusarium population in the field

2017
Sci Rep
PMCID: 5322401
PMID: 28230182
DOI: 10.1038/srep43103
call_split See protocol

[…] Sequences were processed using the RDPipeline initial process to assemble paired-end reads and to remove low quality (Q score < 25) and short reads ( <220 bp). Chimera reads were removed through UCHIME running in de novo mode. Singleto […]

library_books

Four year bacterial monitoring in the International Space Station—Japanese Experiment Module “Kibo” with culture independent approach

2016
PMCID: 5515537
PMID: 28725725
DOI: 10.1038/npjmgrav.2016.7

[…] . The taxonomic affiliation of each OTU was determined using the RDP Classifier at a confidence threshold of 80%. Chao1 index and rarefaction curves based on family-level OTUs were estimated with the RDPipeline (Ribosomal Database Project). The sequences obtained from amplicon sequencing were deposited in the DNA Data Bank of Japan Sequence Read Archive under the accession number DRA004228. […]

call_split

Beneficial Effect of Bidens pilosa on Body Weight Gain, Food Conversion Ratio, Gut Bacteria and Coccidiosis in Chickens

2016
PLoS One
PMCID: 4713076
PMID: 26765226
DOI: 10.1371/journal.pone.0146141
call_split See protocol

[…] on with 16S rRNA primers. Following pyrosequencing (Roche 454), chimeric sequences of the 16S rRNA sequences were removed using Chimera Check []. The trimmed sequences over 300 bp were analyzed using RDPipeline as published []. Briefly, 16S rRNA gene sequence alignment (Aligner), 16S rRNA gene sequence clustering (Complete Linkage Clustering), α-diversity index (Shannon Index and Chao1 estimator), […]

library_books

Eukaryotic opportunists dominate the deep subsurface biosphere in South Africa

2015
Nat Commun
PMCID: 4673884
PMID: 26597082
DOI: 10.1038/ncomms9952

[…] himeras using Bellerophon. Sequences were managed and aligned by RDP. Neighbour-joining phylogenetic trees were generated using RDP. Complete-linkage-clustering and rarefaction curve was managed with RDPipeline. […]

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