Slides from my debriefing of the Cold Spring Harbor Lab Genome Informatics meeting I attended 30 Oct-2 Nov 2013.

1. CSHL Genome Informatics: debriefing
Daniel S. Standage, 5 Nov 2013


2. Themes
 RNA-Seq
 Genomic variation
 Technical details matter
 Reproducibility
 Web-based tools

3. RNA-Seq
 De novo assembly
 Sreeram Kannan, Lior Pachter, David Tse
 Bayesembler
 Quantification
 Sailfish
 Lior Pachter?

4. Genomic variation
 MedSavant
 GEMINI
 SCALPEL: indel ID via NGS
 Others
 Genome rearrangements
 SNPs

5. Technical details matter
 Reproducibility
 Software engineering
 Cyberinfrastructure
 Clear description of methods

6. Software engineering protips
 Version everything
 Test everything (and automate those tests)
 Review everything
 Measure everything
 Engage users

7. Reproducibility
 Don’t rely on a single assembly
 Don’t rely on a single source of annotation
 Genome sequenced twice at deep (60x) coverage,
variants ID’d; only 94% agreed

8. Web-based tools
 Utilize ubiquitous browser
 Most are open source, some offer VM distro
 APIs and SDKs
 integration
 extension
 programmatic access

9. A few talks of interest
 Mario Stanke: comparative gene finding
 Lior Pachter: RNA-Seq methods, units
 Michael Snyder: integrative “Snyderome”
 Sreeram Kannan: RNA-Seq assembly
 Rob Patro: Sailfish
 Chung-chao Hon: natural antisense transcripts