Bioinformatics course for microbial ecologists – mothur pipeline for data analysis

Need help in analyzing huge next-generation sequencing (NGS) data sets? This course offers you the possibility to get familiar with the open-source mothur software package for analyzing amplicon sequencing data. The course will not only focus on technical processing of the NGS data, but also helps the participants to see the ecological aspects. Dr. Patrick Schloss, the organizer and developer of the mothur pipeline, will lead the computer demonstrations.

Time and place


University of Jyväskylä, Jyväskylä, Finland 11.06.2012 to 15.06.2012

Contact person


Preliminay program

Monday 9:00-> ( Lars Paulin, Patrick Schloss, Ari-Matti Saren, Marja Tiirola)

  • NGS sequencing technologies
  • Characterizing microbial communities and searching databases
  • CSC services for NGS data storage and analysis
  • Ion Torrent NGS sequencing demonstration

Tuesday (Patrick Schloss)

  • Using and searching databases
  • R tutorial: Primer on using R

Wednesday (Patrick Schloss)

  • Data curation pipeline of mothur

Thursday (Patrick Schloss)

  • Microbial community analysis using mothur

Friday (Stefan Bertilsson, Lars Paulin and Marja Tiirola)

  • Analysis and annotation of rRNA and protein coding genes, examples
  • Presentations by participants


Assistant professor Patrick Schloss/University of Michigan; Professor Stefan Bertilsson/Uppsala
University; Laboratory engineer Lars Paulin/University of Helsinki; Application specialist Ari-Matti Saren/IT
Center for Science (CSC); Academy research fellow Marja Tiirola/University of Jyväskylä.

Additional information

No course fee for Nordic participants (host institute located in Finland, Sweden, Norway, Denmark or Iceland). NordForsk support covers accommodation between 10.6.-16.6.2012, lunch tickets and coffees, but travels are NOT covered. Participants are presenting their own projects by presentations (10 min) or posters during the course.

Please contact for further information.


Please register by e-mail to before March 15th 2012. Include information of your affiliation, short CV and brief description of your research topic (all in 1 page), and mark the e-mail subject as “Mothur course application”. Participants (max 24) will be selected by allocating places equally to Nordic countries and work groups, and if needed then finally selecting based on the applications. The course is primarily aimed for PhD students, Post docs and senior scientist, but undergraduate students are accepted if there are free places left.