Edinburgh, Scotland

Friday, July 30 through Sunday, August 1st, 2010


Workshop - Friday July 30th, 2010

Location: University of Edinburgh, Pollock Hall Campus

Room: South Hall (


9:00-9:315 AM (Coffee and danish - please pick up and take to your seats.  Bus empty dishes back to the back of the room)


Arrival and introduction: Tom Bruns, D. Jean Lodge


9:15 AM – 10:15


SCATA: Sequence Clustering and Analysis of Tagged Amplicons

Björn Lindahl, Swedish University of Agricultural Sciences, Dept. of Forest Mycology & Pathology, Uppsala, Sweden

Examples of output files




PP lecture


1:15 - 12:00 Noon

Metagenomic analyses and applications in fungal biology: 454 pipelines     

Surendra Kumar, Nordforsk 

Please pre-register at (


12:00 – 1:00 Lunch


1:00 – 3:30

MEGAN - Metagenome Analysis Software  - Daniel Huson

Web site for tutorial and data sets - please download


5:00 PM Social and Barbecue Dinner  Pollock Hall Campus, Abden House – below King Arthur’s Seat.



Workshop - Saturday July  31st, 2010

Location: University of Edinburgh

Room: South Hall


 9AM – 12 noon (10:30-11AM coffee/tea)


MOTHUR – applications to metagenomics

Anthony Amend, University of California, Berkeley (Mothur tutorial pdf)

Download program from

Files: Zip file of downloads


12:30  AM – 1:30 PM Lunch


1:30 PM – 4:30 PM (3:00-3:30 coffee/tea)


Metagenomics cloned-sequences  pipeline used in the LTER study in Alaska -

Lee Taylor, University of Alaska

Downloads and links


Setting up a customized blast client

Shawn Houston, University of Alaska



Sunday, August 1st, 2010

Location: Edinburgh Conference Center (

Genomic methods in fungal community ecology


1:00 Introduction to the session – Jean Lodge


1:10 – 1:30 Ongoing progress in sequencing fungal genomes and application to fungal population biology and ecology 

Jason Stajich  (pdf of talk)



1:45- 2:05 What not to do when doing 454 sequencing

Ari Jumpponen (pdf of talk)


2:15 – 2:35 Chytrid Metatranscriptomics 

Terri Porter and Rytas Vilgalys, Duke University


2:45 – 3:15 New features of UNITE - massBLASTer, 454 pipeline, global ITS key, annotating INSD sequences, etc.

Urmas Kõljalg [] -annotating INSD sequences, global ITS key and future developements.

Henrik Nilsson New features of UNITE II - massBLASTer, 454 pipeline


3:15 - 3:45 Tea/Coffee and Breakout sessions



1.  Automated classification/ How could a centralized reliable infrastructure for fungal metagenomics be constructed?. Andrea Poras-Alfaro

Conrad Schoch, Urmas Kõljalg  (people interested in collaborating on an automated classification system should join this group)


2. Fungal Genomes – priorities.  Jason Stajich and Karl-Henrik Larsson  


3. How can fungal data be made more useful to the community at large.  Is depositing sequences in GenBank/NCBI sufficient? Some of the issues that we may consider would be SRA (Short Read Archive) and how to harvest data from there for meta-analyses, what are the metadata that we should request to be included, what is the best strategy for sequence accession (submit all or examples of unisequences). Tesfaye Wubet

3:45 – 4:15  Breakout session Reports (5-10 mins)