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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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 in publications

 (7)
PMCID: 5911989
PMID: 29193830
DOI: 10.1002/mbo3.557

[…] ad 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., […]

PMCID: 5322401
PMID: 28230182
DOI: 10.1038/srep43103

[…] at bion biotech co., ltd. (nanjing, china). all sequences were deposited in the ncbi sequence read archive (sra) database (accession number: srr3064493)., 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. […]

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., […]

PMCID: 4713076
PMID: 26765226
DOI: 10.1371/journal.pone.0146141

[…] 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 […]

PMCID: 4673884
PMID: 26597082
DOI: 10.1038/ncomms9952

[…] 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., pcr amplification of 18s rrna genepcr amplification of 18s rdna fragments was performed using primer sets: euka (5′-aacctggttgatcctgccagt-3′) and eukb (5′-tgatccttctgcaggttcacctac-3′) […]


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