Data Workflow Overview

Genomics High- Throughput Facility

GenomeAnalyzer IIx

Institute for Genomicsand Bioinformatics

Computation Resources

Storage Capacity

Public Web Servers

● ~ 800 processors● Sun Grid Engine

● ~ 100TB (secured)● Fast drives● 30TB for HTS

● HTTP, FTP● Dedicated hosts● User accounts

HTS: 700GB/day

Bandwidth: 10Gb/s

USER

Sample Analysis Requests(via web interface)

Analysis Results(FTP server)

Data Analysis Workflow

IMAGES2-4 TB

INTENSITIES100-200 GB

Image Analysis

Firecrest

Base Calling

Bustard

BASE CALLS50-100 GB

SEQUENCES+ SCORES20/30 GB

Synthesis

Gerald

GENOMEALIGNMENT

>100 GB

Alignment

ELAND+ Reference Genome

READ COUNTSRead Counting

Casava VDC

Sample-Specific Analysis, Visualization…

e.g. Genome alignment, RNAseq, CHIPseq analysis

Downloadable files for HTS usersFASTQ files

Sequences, Scores (FASTQ)

@HWUSI-EAS1562_0001:8:1:1119:18138#0/1ATATTCTTATATAAAAATATAATTATTTTAATATTTGGTCCTTTCGTACTAAAATAT+HWUSI-EAS1562_0001:8:1:1119:18138#0/1aaY`_aaY^a``[[`a\\\\aaa_^[aaZZWaaaXXY[VYaW^aaaa[aaa]a[a`

@HWUSI-EAS1562_0001:8:1:1119:13476#0/1AGAAAGCTTTGAAAATTATGTATACGCCTCGTAAGCCCAGTCCAAAGTCAAGACCA+HWUSI-EAS1562_0001:8:1:1119:13476#0/1a_^`a`_a[[NOONN__V__`Y^`^X]R[]]]]]Q```Y````__`^W`YVUPR]]

Sequence identifier Raw SequencePhred base calling quality scores(0 to 62 encoded using ASCII 64 to 126)

Genome Alignment (ELAND)

HWUSI-EAS1562_0001:8:1:1119:18138#0/1 ATATTCTTATATAAAAATATAATTATTTTAATATTTGGTCCTTTCGTACTAAAATAT U1 0 147 255 chr1.fa 26532086 F 23G

HWUSI-EAS1562_0001:8:1:1119:13476#0/1 AGAAAGCTTTGAAAATTATGTATACGCCTCGTAAGCCCAGTCCAAAGTCAAGACCA U0 1 0 0 chr12.fa 90535786 F

Sequence identifier

Raw Sequence

Type of match

Number of exact/1-error/2-error matches

Chromosome/Position/Direction

Substitution

Read Counts (Casava VDC)

Matchs with Genes, Exons, Splice junctions

Chromosome Gene Matchs

Files for visualization (GenomeStudio)

Genome alignment, Gene expression,RNAseq and CHIPseq analysis