Data Analysis and Bioinformatics
Background
Like other NextGen sequencing platforms, the Illumina Genome Analyzer II generates a large volume of data. With increased use of this technology globally, solutions for manipulation and analysis of NextGen data are becoming widely available.
For customers without access to their own in-house solutions, GeneWorks offer a range of analysis options suitable for most applications.
Data Formats
The Illumina Genome Analyzer II generates raw data in the form of fluorescence images of clonal DNA clusters. These are processed by our staff through Illumina’s data analysis Pipeline, resulting in sequencing data in the form of large text files of sequence reads and associated base call quality data.
A variety of sequence data formats can be produced by the Illumina pipeline. Most commonly GeneWorks provides fastQ format data (four lines of text per read including ASCII character-encoded quality scores) but other formats are available on request. The volume of data normally provided to a customer on project completion can vary from about a gigabyte for a small project to hundreds of GB for a large genome, and is normally provided on DVD or hard disk.
Analysis Options
In addition to basic data manipulation such as sequence trimming and counting, GeneWorks offers an increasing range of its own analysis solutions using commercially developed software from DNAStar Inc. Central to this is our investment in the SeqMan NGen v1.2 assembler, which is primarily designed to assemble and analyse data from Illumina, 454 and Sanger sequence platforms. NGen allows templated (ie using a close reference sequence) assembly of genome sequence. With advancements in software and associated computer speed, de novo assembly for smaller sized genomes will also become a possibility.
Assemblies made by GeneWorks using NGen can be further analysed using SeqMan Pro, one of the modules from DNAStar’s Lasergene suite (v 7.2 or higher). Please click here for more information and a free demonstration of SeqMan Pro.
GeneWorks also recently announced a partnership with Synamatix Founded in 2002, Synamatix is a specialist NextGen Bioinformatics software tools and services provider based in Kuala Lumpur, Malaysia. Synamatix has developed Synaworks, a set of advanced solutions to analyse data from the Genome Analyzer and other NextGen platforms. For more information on Synamatix solutions for specific applications please contact GeneWorks .
Data Security
GeneWorks realises that integrity, security and confidentiality of customer data is of paramount importance and has measures in place to protect this.