Bioinformatics Services for HT Sequencing

Transcription

1 Bioinformatics Services for HT Sequencing Tyler Backman, Rebecca Sun, Thomas Girke December 19, 2008 Bioinformatics Services for HT Sequencing Slide 1/18

2 Introduction People Service Overview and Rates Resources Hardware Web Site: Sample Submission and Data Download Data Analysis and Software Bioinformatics Services for HT Sequencing Slide 2/18

3 Bioinformatics Service Team Rebecca Sun - Bioinformatics Data Analyst Tyler Backman - Bioinformatics Data Analyst Thomas Girke - The one to blame... Bioinformatics Services for HT Sequencing People Slide 3/18

4 Bioinformatics Services Most time consuming part of HT sequencing projects Most analysis steps can only be handled by powerful servers! Facility provides a wide spectrum of data analysis and pipeline development services for: Primary data analyses Custom data analyses Due to the wide spectrum of data analysis options for the specific needs of each project, we strongly recommend to discuss them in a meeting with the bioinformatics staff. Bioinformatics Services for HT Sequencing Service Overview and Rates Slide 4/18

5 Service Overview Primary data analysis QC of sequencing run Quality filtering and adaptor trimming Basic mapping to reference genome Access to externally and internally developed analysis pipelines and packages Available upon request Online genome browser support Web BLAST server support Custom data analysis Comprehensive custom analysis: annotations, mapping, predictions etc. Specialty algorithms for base calling, alignment, etc. Detailed data analysis reports Statistical analysis Any custom request if reasonable Bioinformatics Services for HT Sequencing Service Overview and Rates Slide 5/18

6 Bioinformatics Service Rates General charges Sequence/quality control: no cost Sequencing run storage on tapes: included in sequencing run Online genome browser and BLAST server support: standard hourly rate (see below) Rates for custom data analysis 1 week projects: $24/hr 1-2 week project: $18/hr Projects >2 weeks: $12/hr Bioinformatics Services for HT Sequencing Service Overview and Rates Slide 6/18

7 Technical Overview Data processed on and served from 16 cpu Linux server Images and sequences archived on tape and RAID array Extended analysis on 256 cpu Linux cluster Bioinformatics Services for HT Sequencing Hardware Slide 7/18

8 HT Sequencing Web Site Submit sequencing projects (collections of samples) View QC reports Download data Obtain additional information on sequencing and data analysis Bioinformatics Services for HT Sequencing Hardware Slide 8/18

9 HT Sequencing Web Site: Navigation Bioinformatics Services for HT Sequencing Web Site: Sample Submission and Data Download Slide 9/18

10 HT Sequencing Web Site: Sample Submission Bioinformatics Services for HT Sequencing Web Site: Sample Submission and Data Download Slide 10/18

11 HT Sequencing Web Site: Sample Details Key/Value pairs describe each sample for future reference Bioinformatics Services for HT Sequencing Web Site: Sample Submission and Data Download Slide 11/18

12 Illumina Pipeline Other tools are available for base calling, alignment, and downstream analysis Bioinformatics Services for HT Sequencing Data Analysis and Software Slide 12/18

13 Flowcell Quality Report Shows read yield and quality Bioinformatics Services for HT Sequencing Data Analysis and Software Slide 13/18

14 HT Sequencing Web Site: Downloading Data Data is provided in many formats Bioinformatics Services for HT Sequencing Data Analysis and Software Slide 14/18

15 Data Formats for Illumina Reads Format Description fastaq sequence text file quality score text file sequences and ASCII quality scores sequences and numeric quality scores Detailed quality scores (4 per base) Sample sequence text file Bioinformatics Services for HT Sequencing Data Analysis and Software Slide 15/18

16 Anno-J Genome Browser Excellent performance for large datasets Bioinformatics Services for HT Sequencing Data Analysis and Software Slide 16/18

17 GBrowse Genome Browser Flexible visualization options Bioinformatics Services for HT Sequencing Data Analysis and Software Slide 17/18

18 Useful Bioinformatic Tools Type Base Calling Alignment Quality Control Digital Gene Expression (DGE) Software Packages Bustard, Alta-Cyclic, Rolexa Eland, Soap, Maq, Bowtie, Novoalign TileQC, BioConductor ShortRead edger Download links on HT Sequencing Site Bioinformatics Services for HT Sequencing Data Analysis and Software Slide 18/18