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SILVAngs specifications

Information


Unique identifier OMICS_13304
Name SILVAngs
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format FASTA
Computer skills Basic
Version 1.6.3
Stability Stable
Maintained Yes

Documentation


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Publication for SILVAngs

SILVAngs citations

 (39)
library_books

Microbiome and Culture Based Analysis of Chronic Rhinosinusitis Compared to Healthy Sinus Mucosa

2018
Front Microbiol
PMCID: 5932350
PMID: 29755418
DOI: 10.3389/fmicb.2018.00643

[…] /ngs/) (Glockner et al., ) using SILVA release version 123 with default settings (ambiguity and homopolymers 2%, OTU clustering 97%, min seq. quality 30%, min length 200 bp, min align. identity 50%). SILVAngs data analysis service uses the SILVA Incremental Aligner (SINA) and to remove contaminations of the dataset with non-rRNA sequences and removes sequences with ambiguity and homopolymers (max. […]

library_books

Long Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field Experiment

2018
Front Microbiol
PMCID: 5816784
PMID: 29487575
DOI: 10.3389/fmicb.2018.00144

[…] f 299 nucleotides (nt) were obtained from the eight analyzed leaf samples derived from eight plots. In summary, 204,704 sequences (32.1%) were rejected, because they failed the quality control of the SilvaNGS pipeline. Finally, 433,922 sequences (7,627–88,073 per sample) were subjected to analysis (Supplementary Table ). A total number of 14,420 OTUs (2.3%) was obtained based on a 98% sequence sim […]

library_books

Planktonic microbial profiling in water samples from a Brazilian Amazonian reservoir

2018
PMCID: 5911997
PMID: 29380948
DOI: 10.1002/mbo3.523

[…] RAST (Metagenomics Analysis) server on November 2014. Reads from the three regions of the16SrRNA from both samples were processed by the NGS analysis pipeline of the SILVA rRNA gene database project (SILVAngs 1.3) (Quast et al., ), according previous work (Ionescu et al., ). Processing of shotgun reads was performed using the metagenomics pipeline (Meyer et al., ) with default options for initial […]

library_books

16SPIP: a comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing

2017
BMC Bioinformatics
PMCID: 5751400
PMID: 29297318
DOI: 10.1186/s12859-017-1975-3

[…] othur, SILVAngs, MEGAN, and AmpliconNoise []. Despite having the vast availability of algorithms, QIIME is widely used in microbial community diversity analysis [], as well as MEGAN [] and Mothur []. SILVAngs [] is a web page analysis tool that based on the SILVA database for the OTU species classification, only supports the maximum 500 M sequencing data. And AmpliconNoise [] is mainly used for 45 […]

library_books

Bacterial Diversity and Biogeochemistry of Two Marine Shallow Water Hydrothermal Systems off Dominica (Lesser Antilles)

2017
Front Microbiol
PMCID: 5722836
PMID: 29255454
DOI: 10.3389/fmicb.2017.02400

[…] aries.py command as implemented in QIIME v1.9.1 (Caporaso et al., ). Processing of raw sequences, including alignment, quality control, dereplication, clustering and classification, was done with the SILVAngs analysis pipeline 1.2 (SILVA SSU Ref dataset 119.1; Quast et al., ). EzBioCloud was used to assign pairwise similarity to the most abundant OTUs against their closest (un)cultured relatives ( […]

library_books

Capturing Early Changes in the Marine Bacterial Community as a Result of Crude Oil Pollution in a Mesocosm Experiment

2017
PMCID: 5745021
PMID: 29187706
DOI: 10.1264/jsme2.ME17082

[…] lculated with defined distance units of 0.03 as the cut-off level. Following this, all non-chimeric sequence reads were processed by the NGS analysis pipeline of the SILVA rRNA gene database project (SILVAngs 1.3) (). Each sequence was aligned using the SILVA Incremental Aligner tool (SINA v1.2.10 for ARB SVN [revision 21008]) (). The initial steps of quality control () were performed and identica […]

Citations

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SILVAngs institution(s)
Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany; Jacobs University Bremen gGmbH, School of Engineering and Science, Bremen, Germany; Ribocon GmbH, Bremen, Germany
SILVAngs funding source(s)
This work has been supported by the Max Planck Society and the Deutsche Forschungsgemeinschaft.

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