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Illumina’s Genome Analyzer Software Suites

Illumina’s Genome Analyzer Software Suites. Josh Hanna *All images adapted from www.illumina.com. Overview. System Software Sequencing Control Software Pipeline Software CASAVA GenomeStudio Data Analysis Software DNA Sequencing Module RNA Sequencing Module ChIP Sequencing Module.

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Illumina’s Genome Analyzer Software Suites

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  1. Illumina’s Genome AnalyzerSoftware Suites Josh Hanna *All images adapted from www.illumina.com

  2. Overview • System Software • Sequencing Control Software • Pipeline Software • CASAVA • GenomeStudio Data Analysis Software • DNA Sequencing Module • RNA Sequencing Module • ChIP Sequencing Module

  3. System Software: Sequencing Control Software • Tools for managing and executing Genome Analyzer experiment runs. • Flexible instrument control • Can export intensities or base calls and quality statistics into Pipeline Software. • Flexible data migration and archiving. • Base calling occurs simultaneously and is complete within hours of the sequencing run • Real-time feedback.

  4. System Software: Pipeline Softare • Performs base calling and read alignment. • Takes data from the SCS. • Runs on Linux. • Open source. • Data can be exported into CASAVA and GenomeStudio • Maximizes number of clusters used to generate sequence data with automated image calibration • Filters reads using cluster intensity scoring algorithms

  5. System Software: CASAVA • Consensus Assessment of Sequence and Variation (CASAVA) • Captures summary information for resequencing and can condense results • Compact data structures can be exported into GenomeStudio or other third-party tools • Functions: • Create genomic builds • Call SNPs • Detect indels • Count reads

  6. GenomeStudio: DNA Seqencing Module • Visualizes data for single and paired-end DNA sequencing experiments • Results can be explored at any level. • Visualizes alignment of stacked reads against a reference genome • Can be used to monitor coverage • Matches discovered cSNPs with dbSNPs via reports • Can be used to identify novel SNPs

  7. GenomeStudio: RNA Sequencing Module • Visualizes aligned reads to a reference sequence • Splice junction sets, abundant sequence set, etc. • Analyze and visualize results of counts of exons, genes, and splice junctions found in sample • Perform whole transcriptome analysis • Aggregate data from multiple lanes of a flow cell, and count the abundance of reads falling within specific exons, genes, and splice functions

  8. GenomeStudio: ChIP Sequencing Module • Map global binding sites for DNA-associated proteins • Identify differential binding levels between experimental groups • Transfer sequence data from Pipeline output • Align and visualize sequence reads against genome browser • Scan and explore results at any level • Combine multiple experiments in a single ChIP-Seq project to maximize coverage

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