Launch of 16S analysis workflow
The 16S rRNA gene is present in all bacteria and archaea. Including both consistent and highly variable regions, the gene is ideal for sequence-based identification of these organisms, particularly in metagenomics (mixed samples).
Oxford Nanopore has now released a workflow to enable users of its sequencing technologies to classify mixed samples and obtain accurate results for single reads at the genus level.
The workflow is designed to BLAST basecalled sequence against the NCBI 16S bacterial database, which contains 18,927 16S sequences from different organisms. Each read is classified based on % coverage and identity*.
The 16S workflow will be useful to any researcher interested in identifying pathogens in a mixed sample or understanding the composition of a microbial community; both already thriving subjects of research within the nanopore community.
Further reading:
- 16S analysis using Oxford Nanopore technology
- 16S Workflow: post on the Nanopore Community (login, for users of nanopore technology)
- Oxford Nanopore poster, December 2016. “Barcode of life: simple laboratory and analysis workflows for 16S and CO1 analysis”
- Oxford Nanopore poster, December 2016: "DNA extraction and library preparation for rapid genus- and species-level identification, with or without PCR"
- Publications focusing on pathogen or microbial analysis
- Publications focusing on metagenomics analysis
*This is in contrast to the What's In My Pot (WIMP) application, which uses kraken to align all reads from a mixed sample to an NCBI database of bacteria, viruses and fungi. Between the WIMP and 16S workflows, nearly all scenarios for taxonomic assignment of small-genome species are covered.