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Chao Xie, Chin L Goi, Daniel H Huson, Peter F Little, and Rohan B Williams (2016)

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys

BMC Bioinformatics, 17(19):277–282.

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.

10.1186/s12859-016-1378-x