Title: "Second generation sequencing: An overview plus potential benefits and pitfalls"
Speaker: Rick Westerman, Bioinformatics Specialist, Genomics Facility, Purdue University
Place: Mechanical Engineering (ME) 161; October 21, 2008, Tuesday, 4:30pm


The advent of second generation (2nd gen) sequencing during the last couple of years has been rapidly displacing the monopoly enjoyed by Sanger sequencing. The current 2nd gen systems generate much more data at a lower cost than previous sequencers. This massive amount of data is presenting new challenges in data analysis as well as spurring on innovative methods in genomic research. The Genomics Facility at Purdue has two of the three common 2nd gen "sequencing by synthesis" systems -- the Roche FLX/454 system and the ABI SOLiD system (we do not have the Illumina/Solexa system.) My talk will present an overview of 2nd gen sequencing technology, cover some of the innovative algorithms that are being produced worldwide, and then delve into some of the real life problems and solutions that we have encountered while using our 2nd gen systems.

Suggested reading:
1) Next-Generation Sequencing: The Race is on. Cell 132, March 7, 2008. Andreas von Bubnoff.

2) Next-Generation DNA Sequencing Methods. Annual Review of Genetics and Human Genetics, 9:387-402. Elaine R Mardis.

3) Bioinformatics challenges of new sequencing technology. Trends in Genetics. Volume 24, Issue 3, March 2008, Pages 142-149. Mihai Pop, Steven L. Salzberg.

4) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research. (pre-print) Sep 25, 2008. Stephan Ossowski, et. al

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