Quickly go from image capture to interactive analysis using the customizable Genome Analyzer System data analysis workflow engine. The Sequencing Control Software (SCS) and Consensus Assessment of Sequence and Variation (CASAVA) software programs convert raw image data into intensity scores, base calls, quality scored alignments, and additional formats for downstream analysis, rapidly transforming data into biologically relevant information.
Open access to the source code and a flexible software architecture allow you to customize the Genome Analyzer workflow engine to meet your specific analysis needs.
Genome Analyzer
Important Information
Sequencing Control Software
Provides real-time tracking of a sequencing run; processes images in real time and reduces the need for costly data storage; generates intensity values and base calls.
The Illumina Sequence Control Software (SCS) with Real Time Analysis (RTA) provides a complete set of software tools for managing and executing Genome Analyzer experiment runs, from sample tracking and initial run set up through completion of primary analysis. SCS enables completely flexible yet unattended instrument operation, while its real-time reports and graphs give continuous run feedback. Image analysis, base calling, and base call quality calibration are accomplished automatically during the run with the Real Time Analysis module - when the run completes, the data is ready.
| SCS Highlights | |
|---|---|
| Flexible Instrument Control | Easily choose from a number of recipes for various sequencing applications |
| Compatible Design | Readily import intensities or base calls and quality statistics into the Genome Analyzer Pipeline Software |
| Flexible Data Migration and Archiving | Reduce raw sequence data into a compact base and quality format |
| Efficient and Fast Results | Minimize time spent in subsequent analysis steps; base calling occurs simultaneously and is complete within hours of the sequencing run |
| Real-Time Feedback | Monitor run performance during the sequencing run |
Pipeline Software
Performs base calling and read alignment.
Genome Analyzer Pipeline software is a customizable analysis engine that takes you from Sequencing Control Software (SCS) output to quality scored alignments. Developed in collaboration with many of the world's leading sequencing centers, the Pipeline software is designed to scale to meet the needs of even the most prodigious facilities.
This software runs on numerous Linux operating systems and is an open source program, making it entirely customizable. For customers desiring a ready-to-use system, a Pipeline Analysis Server is also available.
Pipeline data can be easily imported into CASAVA and GenomeStudio software, allowing you to explore your data from multiple genetic analysis applications and obtain a complete picture of the genome.
| Pipeline Software Highlights | |
|---|---|
| Complete | Maximize the number of clusters used to generate sequence data with automated image calibration |
| Reliable | Filter for high-quality reads using accurate cluster intensity scoring algorithms |
| Accurate | Minimize the propagation of downstream sequencing errors with quality-calibrated base calls |
| Customizable | Reduce the need for elaborate computer infrastructures with highly optimized genomic alignment tools |
| Flexible | Identify structural variants and sequencing repetitive regions with intelligent paired-end logic |
| Pipeline System Requirements | |
|---|---|
| Operating System | Linux |
| Processors | At least two; eight nodes optimal |
| Storage Capacity | > 2 TB |
CASAVA
Creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs.
Illumina's Consensus Assessment of Sequence and Variation (CASAVA) software captures summary information for resequencing and counting studies and places the data in a compact structure for visualization within GenomeStudio Software or publicly available analysis tools. CASAVA can create genomic builds, call SNPs, detects indels, and count reads from data generated from one or more runs of the Genome Analyzer across a broad range of sequencing applications. Find out more in the Improved Accuracy for ELAND and Variant Calling Technical Note.
CASAVA now supports Nextera dual indexing.
| CASAVA Highlights | |
|---|---|
| Aggregation | Condense real results from many runs of a resequencing or counting experiment |
| Consensus Calling | Generate base-calls for every position in the genome where supporting evidence is found |
| Polymorphism Detection | Produce SNP reports for use in association studies and for correlation with microarray experiments |
| Indel Detection | Identify insertions/deletions of up to length 100bp from paired-end data |
| Counting Statistics | Generate lists of counts for reads that align to specific genomic entities such as genes, exons, and splice junction |
| CASAVA System Requirements | |
|---|---|
| Operating System | Linux |
| Processors | 4 quad-core processors (recommended) |
| Memory Requirements |
2GB per core |
Third-Party Data Analysis Tools
The evolution of next-generation sequencing technology will continue to require collaboration among researchers, thought leaders, and industry. Illumina encourages the open exchange of information and ideas, and we are committed to rapidly delivering solutions that will maximize your scientific success.
Below you will find tools developed by Illumina sequencing customers that you can use to analyze your Genome Analyzer data. These software applications* are designed to be used for a variety of sequencing applications such as resequencing, ChIP-Seq, and Digital Gene Expression. Our customers have made these tools freely available to you.
Genome Alignment Browsers
- Gbrowse - Genomic Browsing, Generic Model Organism Database Project
http://www.gmod.org/wiki/index.php/Gbrowse - UCSC Browser - Genome browsing and comprehensive annotation, Generic Model Organism Database Project
http://genome.ucsc.edu/goldenPath/help/customTrack.html - Staden Tools (GAP4, TGAP) - Alignment and Visualization for Small Data Sets, James Bonifield (initially developed by Rodger Staden), Wellcome Trust Sanger Institute
http://sourceforge.net/projects/staden/
Alignment and Polymorphism Detection
- BFAST – Blat-like Fast Accurate Search Tool, Nils Homer, Stanley F. Nelson and Barry Merriman, University of California, Los Angeles
http://genome.ucla.edu/bfast - MAQ – Mapping and Assembly with Quality, Heng Li, Sanger Centre
http://maq.sourceforge.net/maq-man.shtml - Bowtie - An ultrafast memory-efficient short read aligner, Ben Langmead and Cole Trapnell, Center for Bioinformatics and Computational Biology, University of Maryland
http://bowtie-bio.sourceforge.net/
Genomic Assembly
- Velvet – De novo assembly of short reads, Daniel Zerbino and Ewan Birney, EMBL-EBI
http://www.ebi.ac.uk/~zerbino/velvet/ - SSAKE – Assembly of short reads, Rene Warren, et al, British Columbia Cancer Agency
http://bioinformatics.oxfordjournals.org/cgi/content/full/23/4/500 - Euler – Genomic Assembly, Pavel Pevzner and Mark Chaisson, University of California, San Diego
http://nbcr.sdsc.edu/euler/
ChIP Sequencing
- ChIP-Seq Peak Finder, Barbara Wold, Cal Tech and Rick Meyers, Stanford University
http://woldlab.caltech.edu/html/software/
Digital Gene Expression
- Comparative Count Display, Alex Lash, NIH
ftp://ftp.ncbi.nlm.nih.gov/pub/sage/obsolete/bin/ccd/ - SAGE DGED Tool, Cancer Genome Anatomy Project
http://cgap.nci.nih.gov/SAGE/SDGED_Wizard?METHOD=SS10,LS10&ORG=Hs
* Illumina cannot guarantee the accuracy of the data obtained from the websites above. We do not provide support for third-party software tools.