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Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

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Ribosomal Database Project: data and tools for high throughput rRNA analysis.

James R Cole¹, Qiong Wang, Jordan A Fish

¹Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA, Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA, Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Biological Sciences, Western Illinois University, Malcomb, IL 61455, USA and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

Nucleic Acids Research

|November 30, 2013

Summary

This summary is machine-generated.

The Ribosomal Database Project (RDP) now offers fungal rRNA gene data and enhanced tools for analyzing large, high-throughput sequencing datasets. These resources support diverse research in microbial ecology, taxonomy, and phylogenetics.

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Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

The Ribosomal Database Project (RDP) is a crucial resource for accessing aligned and annotated rRNA gene sequence data.
RDP tools facilitate the analysis of rRNA gene sequences within a standardized framework.
Applications span human health, microbial ecology, environmental microbiology, taxonomy, and phylogenetics.

Purpose of the Study:

To announce the inclusion of fungal large subunit rRNA genes in the RDP.
To detail updates to RDP tools (Classifier, Aligner) for fungal data compatibility.
To introduce enhanced tools for analyzing large-scale, high-throughput sequencing data.

Main Methods:

Expansion of the RDP database to include fungal large subunit rRNA genes.
Updates to existing RDP analysis tools to support the new fungal collection.
Development of new tools to facilitate the analysis of high-throughput sequencing data, including single-stranded and paired-end reads.

Main Results:

The RDP now provides comprehensive rRNA gene data for bacteria, archaea, and fungi.
RDP tools are updated to analyze diverse rRNA gene collections.
Release 11 offers expanded capabilities for high-throughput data analysis, supporting modern sequencing technologies.

Conclusions:

The RDP continues to be an essential resource for rRNA gene analysis.
The expanded fungal collection and enhanced high-throughput analysis tools broaden the RDP's utility.
Availability of RDP tools as open-source packages increases accessibility for researchers with high-volume or custom analysis needs.