SCATA: Sequence Clustering and Analysis of Tagged Amplicons

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

http://scata.mykopat.slu.se

Examples of output files

all_clusters.txt

all_tag_by_cluster.txt

all_tags.txt

PP lecture

1:15 - 12:00 Noon

Metagenomic analyses and applications in fungal biology: 454 pipelines     

Surendra Kumar, Nordforsk 

Please pre-register at (http://www.bioportal.uio.no/)

12:00 – 1:00 Lunch

1:00 – 3:30

MEGAN - Metagenome Analysis Software  - Daniel Huson

Web site for tutorial and data sets - please download  http://www-ab.informatik.uni-tuebingen.de/software/megan/fesin-2010/

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   http://www.mothur.org/wiki/Download_mothur

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

Lecture

Sunday, August 1^st, 2010

Location: Edinburgh Conference Center (http://www.imc9.info/)

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 [urmas.koljalg@ut.ee] -annotating INSD sequences, global ITS key and future developements.

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