Georg Steinert

marine ecology and systematics

16S rRNA analyses

Short 16S rRNA analyses tutorials - links - useful packages - this pipeline below feels like a fractal - I will try to zoom in at several points (while I work on this, please click to enlarge).

All tools, packages and sites described here (and more), can be found under the links section - and don't forget to check out their tutorials!

In addition I'll list and link some of the methods paper describing the specific use and approach:

• mothur:
  'Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities' - Schloss et al. 2009
• qiime:
  'QIIME allows analysis of high-throughput community sequencing data' - Caporaso et al. 2010
• sina:
  'SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes' - Pruesse et al. 2012
• silva:
  'The SILVA ribosomal RNA gene database project: improved data processing and web-based tools' - Quast et al. 2013
• oligotyping:
  'Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data' - Eren et al. 2013
• multicola:
  'Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets' - Gobet et al. 2010
• phyloseq:
  'Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data' - McMurdie et al. 2012
• indicspecies:
  'Improving indicator species analysis by combining groups of sites' - De Caceres et al. 2010

Also, please read this paper if you are interested in multivariate analyses in microbial ecology: Multivariate analyses in microbial ecology by Alaban Ramette (2007) and if you are hooked, then take a look at this paper and the corresponding homepage: A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses Buttigieg & Ramette 2014 - GUSTA ME.