ISMB 2008 Special Interest
Group on Algorithms for Next Generation Sequencing Technologies Schedule:
8:40-10:15am: Session 1:
Welcome & Read Mapping
10:15-10:45am: Coffee
break
10:45am-12:30pm: Session
2: Imaging and Data Management; SNP calling
12:30-1:45pm: Lunch
1:45pm-3:30pm: Session 3:
Analysis & Structural Variation
3:30-4:00pm: Coffee break
4:00pm-6:15pm Session 4:
Assembly & Keynote
Presentations:
Read
Mapping:
PASS: A Fast Algorithm for
Illumina/SOLiD Sequence Alignment with Guaranteed Recall
Manhong Dai, Justin Wilson,
Stanley Watson and Fan Meng
Optimal Spliced Alignments of
Short Sequence Reads
Fabio De Bona, Stephan Ossowski,
Korbinian Schneeberger, Gunnar Ratsch
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, and Jingwe Ni
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 for Next-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
SNP calling:
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
SNP calling by next-generation
sequencing on draft genomes
Sebastian Frohler and Christoph Dieterich
Analysis:
Taxonomical and Functional
Characterization of Ultra-Short Reads from Microbial Metagenomes using the q-gram
Index
Wolfgang Gerlach
Statistically-corrected
Counting of Short Reads for Digital Gene Expression Profiling
Doron Lipson, Tal Raz, Alix Kieu, Marie Causey, Ed Thayer
Structural Variations:
Personal Genomics Using the
Next Generation Sequencing Technologies
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
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
Keynote:
John McPherson
Director of Cancer Genomics and
Senior Principal Investigator,
Ontario Institute for Cancer Research