RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys.
BACKGROUND
Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis.


RESULTS
Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion.


CONCLUSIONS
RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs.
Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 117456, Singapore. xiechaos@gmail.com.|Current address: Human Longevity Inc, Singapore, Singapore. xiechaos@gmail.com.
Chao
C
Xie
Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 117456, Singapore.
Chin Lui Wesley
CL
Goi
Centre for Bioinformatics, Tuebingen University, Tuebingen, 72076, Germany.|Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.
Daniel H
DH
Huson
Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 117456, Singapore.|Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.|Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.
Peter F R
PF
Little
Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 117456, Singapore.
Rohan B H
RB
Williams
D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D004275:DNA, Ribosomal / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D054892:Metagenome; D056186:Metagenomics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012337:RNA, Ribosomal, 18S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D059467:Transcriptome
D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S
Microbial community profiling; Microbial ecology; Sequence analysis; Short subunit ribosomal RNA