The Genome Sequencer FLX System includes software packages that process raw images into PHRED-like scored high-quality reads
The chemiluminescent signal resulting from a sequencing reaction is captured by the CCD camera. Subsequently, the signal undergoes image processing such as background substraction and normalization. In addition, a Phred-like quality score is calculated. The data-processing output for mapping and assembly includes normalized signals, flowgrams, and base-called consensus sequences. All raw data is accessible, and the file formats are compatible with publicly available sequencing analysis tools.
Figure 11: Data processing and analysis tools of the Genome Sequencer FLX System.
GS De Novo Assembler Software
The GS De Novo Assembler software generates a consensus sequence of the whole DNA sample by assembly of de novo shotgun sequencing reads into contigs and subsequent ordering of these contigs into scaffolds. Contig ordering is done by generation and assembly of paired-end reads. The GS De Novo Assembler Software allows for de novo assembly of up to 120 megabases of sequencing data, enabling:
- De novo sequencing of whole genomes from humans, plants, yeasts, bacteria, fungi, viruses, YACs, BACs, fosmids
GS Reference Mapper Software
The GS Reference Mapper Software generates a consensus DNA sequence by mapping, or alignment, of the sequencing reads to a reference sequence. In addition, it generates a list of high-confidence mutations by identification of individual bases that differ between the generated consensus DNA sequence and the reference sequence. The GS Reference Mapper Software facilitates the resequencing of up to three Gigabases of sequencing data, enabling:
- Resequencing of whole genomes from humans, plants, yeasts, bacteria, fungi, viruses, YACs, BACs, fosmids
- Analysis of Disease Associated Regions
GS Amplicon Variant Analyzer Software
The GS Amplicon Variant Analyzer Software compares amplicon sequencing reads to a reference sequence. Multiple alignment of several hundreds of clonal amplicon reads (ultra-deep amplicon sequencing) and comparison of these reads against a reference sequence allows for the detection of rare sequence variations even in heterogeneous specimens. The GS Amplicon Variant Analyzer Software enables:
- Discovery of SNPs on a population level
- Detection of rare somatic mutations
- Analysis of DNA methylation patterns
- Viral subtyping
GS Run Browser Software
The GS Run Browser Software is an interactive application that displays the results of a sequencing run as well as raw images and graphic representations of various metrics files. GS Run Browser Software can be used to assess the general quality of a run, and therefore is a useful tool for troubleshooting if problems are observed. The application also facilitates evaluation of the results of titration experiments. Data generated by GS Run Browser Software can be exported to an Excel spreadsheet.
Third party software tools
In addition to the software packages provided with the Genome Sequencer FLX System, third party software tools enable analysis of data generated from running the following applications on the Genome Sequencer FLX System:
- Analysis of full length cDNA
- Identification and quantification of transcrips
- Investigation of 16S rRNA in microbial diversity studies
- Analysis of small non coding RNAs
- ChIP sequencing
