Keynote:

John McPherson

Director of Cancer Genomics and Senior Principal Investigator,

Ontario Institute for Cancer Research

Imaging/Data Management:

Alta-Cyclic – an improved Solexa base caller for longer and more accurate reads

Yaniv Erlich, Partha P. Mitra, W. Richard McCombie, Gregory J. Hannon

Swift: Open Source Primary Data Analysis forNext-generation sequencers

Nava Whiteford, Tom Skelly, Irina Abnizova, Clive Brown

NCBI Short Read Archive Format & SDK

Vladimir Alekseyev, Kurt Rodarmer, and the NCBI Short Read Archive team

Read mapping/SNP calling:

PASS: A Fast Algorithm for Illumina/SOLiD Sequence Alignment with Guaranteed Recall

Manhong Dai, Justin Wilson, Stanley Watson Fan Meng

Optimal Spliced Alignments of Short Sequence Reads

Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, Gunnar Ratsch

Using UHTS to detect somatic mutations

Christian Iselli , Stylianos Antonarakis, Jacqui Beckmann, Andy Simpson, Jean-Louis Blouin, Siv Fokstuen, Daniel Robyr, Carlo Rivolta, Jacques Rougemont, Ioannis Xenarios, Brian Stevenson, Victor Jongeneel, Andrew Sharp, Donata Rimoldi, Felix Naef

SHRiMP: The Short Read Mapping Package

Stephen M. Rumble, Vladimir Yanovsky, Michael Brudno

The SOLiD system resequencing alignment software suite: matching, pairing and indel finding

Zheng Zhang, Heather Peckham, Jingwe Ni

SNP calling by next-generation sequencing on draft genomes

Sebastian Frohler, Christoph Dieterich

Analysis:

Statistically-corrected Counting of Short Reads for Digital Gene Expression Profiling

Doron Lipson, Tal Raz, Alix Kieu, Marie Causey, Ed Thayer

Taxonomical and Functional Characterization of Ultra-Short Reads from Microbial Metagenomes using the q-gram Index

Wolfgang Gerlach

Assembly:

A Scalable Short Read Assembler - ABySS

Inanc Birol, Jared Simpson, Shaun Jackman, Kim Wong, Steven Jones

Short Read Fragment Assembly with EULER-SR

Mark Chaisson, Dumitru Brinza, Pavel Pevzner

FuzzyPath – a hybrid de novo assembler using mixed Solexa and 454 short reads

Zemin Ning

Consensus Computation on Segments

Tobias Rausch, Anne-Katrin Emde, Knut Reinert

Structural Variation

Personal Genomics Using the Next Generation SequencingTechnologies

Can Alkan, Fereydoun Hormozdiari, Gozde Aksay, Jeffrey M. Kidd, Onur Mutlu, S. Cenk Sahinalp, Evan E. Eichler

Fine-scale mapping of copy number alterations with next generation sequencing

Derek Y. Chiang, Gad Getz, David Jaffe, Xiaojun Zhao, Carsten Russ, Chad Nusbaum, Matthew Meyerson, Eric S. Lander

Identifying Structural Variation Using Next Generation Sequencing Data

Seunghak Lee, Elango Cheran, Michael Brudno