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rRNASelector specifications


Unique identifier OMICS_02620
Name rRNASelector
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability No
Maintained No


No version available

Publication for rRNASelector

rRNASelector citations


EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

Nucleic Acids Res
PMCID: 5753268
PMID: 29069476
DOI: 10.1093/nar/gkx967

[…] sers transition from one site to the other.The analysis pipeline underwent a more substantial update in August 2017 to version 4.0 (Figure ), with the entire taxonomic profiling section replaced. The rRNASelector based component (), which was previously used to identify 16S rRNA genes, was replaced with Infernal () (running in HMM-only mode) using a library of ribosomal RNA models from Rfam 12.2 ( […]


ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services

PMCID: 5461914
PMID: 28620454
DOI: 10.5256/f1000research.11253.r19670

[…] onger single reads (where appropriate) and performs taxonomic classification and functional analysis on unassembled sequences. Despite the presence or absence of sequence assembly, both pipelines use rRNASelector for the identification of 5S, 16S and 23S rRNA sequences, before passing extracted rRNAs to taxonomic classification tools. EMG uses QIIME with Greengenes and a closed-reference OUT pi […]


An evaluation of the accuracy and speed of metagenome analysis tools

Sci Rep
PMCID: 4726098
PMID: 26778510
DOI: 10.1038/srep19233

[…] rom BioPython and trimmomatic, clustered to remove duplicates using UCLUST , and repeats are masked using RepeatMasker. Paired end reads are joined using SeqPrep. Potential rRNA genes are found using rRNAselector, and the taxonomy is predicted from these using QIIME against RDP and GreenGenes. Protein coding genes are predicted using FragGeneScan, and the functional annotations are added using Int […]


Web Resources for Metagenomics Studies

PMCID: 4678780
PMID: 26602607
DOI: 10.1016/j.gpb.2015.10.003

[…] through ENA’s Webin tool or ISAcreator. The EBI Metagenomics analysis pipeline includes trimming and quality checks to remove artifacts and streamline of the data. The processed reads are analyzed by rRNAselector and QIIME to predict taxa, followed by functional assignment by a composite protein database called InterProScan. EBI Metagenomics is well suited for the analysis of shotgun and marker-ge […]


Metagenomics: Tools and Insights for Analyzing Next Generation Sequencing Data Derived from Biodiversity Studies

Bioinform Biol Insights
PMCID: 4426941
PMID: 25983555
DOI: 10.4137/BBI.S12462

[…] consensus, mutually accepted standard. EBI Metagenomics offers a dual shotgun and marker gene analysis service. It allows the extraction of rRNA data from shotgun metagenomic data using tools such as rRNASelector for concurrent marker metagenomic analysis. It therefore supports additional 16S rRNA-based analysis tools such as Qiime (see section on Marker Gene Metagenomics) for the efficient taxono […]

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rRNASelector institution(s)
Interdisciplinary Graduate Program in Bioinformatics, Seoul National University, Seoul, Korea

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