1. Next Generation Sequencing pipeline: a joint LONI – BIRN [UCLA – UCI] collaborative project F. Macciardi – March 16, 2011

2. Pipeline: the concept from sequencing to interpretation of results Wet lab Seq data production DNA, RNA, ChiP [all platforms] Dry lab 1 Data Analysis 1 QC Coverage Callability …. Data Analysis 2 Visualization SNP calls CNV / indels specific motifs Dry lab 2 Data Analysis 1st level results interpretation Sys bio 1st level results interpretation & modeling Dry lab 3 Wet lab Seq data production DNA, RNA, ChiP [all platforms] Molecular Bioinformatics Step 2LONI - BIRN pipeline proposal Step 1

3. Alignment & Assembly * Bioinformatics / Dry Lab 1 & 2 - Step 1.BAM QC, Data Cleaning Visualization SNPs CNVs DNA motifs Signatures Workflow 1Workflow 2 (in progress) Workflow 3Workflow 4 … NGS Pipeline: general plan

4. LONI - BIRN PIPELINE protocol design tool installation module definition workflow implementation workflow validation, and dissemination Implementation of Genomics and Informatics Pipeline Protocols

5. NGS Pipeline workflow 1: Alignment and Assembly

6. NGS Pipeline editing & redesign

7. NGS Pipeline: QC control (in progress)

8. LONI - BIRN PIPELINE Wiki

9. LONI - BIRN PIPELINE paper in writing to be submitted soon …