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.