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3rd June 2008

3rd June 2008, 12:00 PM
Location: Main Seminar Room, MRC HGU, Western General Hospital, Edinburgh
Host: Colin Semple
Parking: It's possible, though far from easy, to find a parking space on the hospital campus. But probably the best option is to park in a neighbouring street such as craigleith hill avenue or carrington road - they have loads of pay and display spaces

Participants
Please, add your name to the participants list if you are planning to come, and whether you would prefer a veggie option.

Agenda
1.Introduction to wiki
2.Future meeting dates (should we have one in July as well?)/topics/speakers
3.Suggested presentations:
Topic proposed by
Assembling bacterial genomes using Edena, Velvet, and SSAKE, Urmi Trivedi
Quality characteristics and biases in Solexa data, Sujai Kumar
Informatics for a Digital Gene Expression study of a worm without a sequenced genome, Mark Blaxter
Resources for next gen sequencing bioinformatics, Colin Semple
Solexa sequencing for Plasmodium chabaudi, Axel Martinelli
Hybrid Sanger + 454 WGS assembly of bacterial genomes, Tony Travis

Talks
How to spot a bad Solexa run in the wild and what to do when you have caught it, Sujai Kumar (The Gene Pool, University of Edinburgh) Text dump

Solexa sequencing of a malarial parasite (P.chabaudi): Challenges and opportunities, Axel Martinelli (University of Edinburgh). Text dump.
Hybrid Sanger + 454 WGS assembly of bacterial genomes, Tony Travis and Rustam Aminov (Rowett Research Institute, Aberdeen). Text dump. Additional papers relevant to Tony's talk: chevreux_thesis_mira.pdf goldberg_smd-2006.pdf han_cs-2006.pdf
De novo assembly from Illumina/Solexa short reads: Assemblers and trends, Urmi Trivedi, The GenePool. Text dump.
Digital tag sequencing using Solexa, Mark Blaxter, The GenePool. Text Dump.
A short survey of short read software, Colin Semple (MRC HGU). Text dump.