High-Resolution Microbiome Informatics Meeting, 2015 (Sat, Mar 14, 2015)
A small-scale meeting to make a statement about high-resolution.
In a nutshell
Oligotyping is a computational method that helps microbial ecologists to investigate concealed diversity within their operational taxonomic units at an extremely precise level by utilizing very subtle variations among 16S Ribosomal RNA gene sequences. A key article to quickly understand its ecological implications is here.
For mothur users (courtesy of Michelle Berry): mothur2oligo
For QIIME users (courtesy of James Meadow): qiime2oligo
All posts oligotyping
New insights into microbial ecology through subtle nucleotide variation (Thu, Feb 12, 2015)
A summary of the oligotyping special topic in Frontiers In Microbiology
From QIIME to Oligotyping (Thu, Oct 16, 2014)
A solution by James Meadow
Oligotyping and alignment (Sun, Sep 14, 2014)
Answers to some of the questions that have been asked frequently
A Docker image for oligotyping (Tue, Sep 02, 2014)
For people who does not want to install the pipeline
Installing the oligotyping pipeline (Sat, Aug 16, 2014)
Installing the pipeline shall not be a PITA.
Oligotyping analysis of the human oral microbiome (Wed, Jun 25, 2014)
In which we oligotyped the entire oral microbiome data generated by the HMP...
Frontiers in Microbiology Special Topic (Thu, Dec 12, 2013)
A special topic for oligotyping
How to oligotype: Best practices (Mon, Nov 04, 2013)
Flowchart of oligotyping...
Methods paper for oligotyping is out! (Wed, Oct 16, 2013)
It is published in Methods in Ecology and Evolution...
Network analysis of the human oral microbiota using oligotypes (Fri, Mar 29, 2013)
The oligotyping pipline generates Gephi-compatible network descriptions.
Sewage reflects the distribution of human faecal Lachnospiraceae (Thu, Feb 28, 2013)
A study that shows the connection between human microbiome and the sewage
Basic sample mapping with oligotyping (Mon, Feb 04, 2013)
If you have a categorical mapping file, the oligotyping pipeline can deliver more
Oligotyping Pipeline Explained (Fri, May 11, 2012)
How to install, and how to start using the oligotyping pipeline
A Success Story: Gardnerella Vaginalis Profiles Among Sexual Partners (Wed, May 02, 2012)
The first story we recovered using oligotyping