Next-Generation Sequencing Analysis

Data Acquisition and Basic Analyses: Illumina

Illumina Miseq Reporter Software

The MiSeq system is the first desktop sequencer to offer a fully integrated sequencing ecosystem and provides automated downstream secondary analysis following basecalling by the MiSeq system. After defining a workflow in Illumina’s Experiment Manager, the MiSeq Reporter software launches automatically post-sequencing to perform a variety of anlyses: library QC, demultiplexing, generation of FASTQ files, alignment, variant detection, and VCF generation.

Available workflows for the software include:

  • Amplicon DS
  • Assembly
  • Enrichment
  • FASTQ Generation Library QC
  • Metagenomics
  • PCR Amplicon Resequencing
  • Small RNA
  • Targeted RNA
  • TruSeq Amplicon

Illumina Sequencing Analysis Viewer (SAV) Software

Assessing the quality of a sequencing run in real-time is essential to proper maintenance, operation, and evaluation of NGS experiment quality. Illumina’s SAV provides a real-time analysis (RTA) software solution for viewing critical quality metrics on the Illumina sequencing system. Of the multitude of metrics viewable in the software, SAV allows for live identification of flow cell over/under-clustering, monitoring cycle-to-cycle intensities, base-calling quality, read quality, and error rates. In addition to monitoring live run quality, the SAV software allows for quick and easy assessment of post-run quality metrics.

Illumina VariantStudio™ 2.2

The Illumina VariantStudio data analysis software application enables researchers to quickly identify and classify disease-relevant variants, and then communicate significant findings in a structure report. Following secondary analysis and VCF generation in MiSeq Reporter, VariantStudio 2.2 allows for seamless assessment of variant calling, annotation, classification, and reporting. Coupled with BaseSpace, VariantStudio provides virtually instantly accessible reports for collaborative sequencing projects.

Advanced Analyses: Qiagen

Biomedical Genomics Workbench 4

Biomedical Genomics Workbench is a comprehensive and accurate data analysis platform that enables you to find the signal in the noise in your cancer and hereditary disease NGS data. With its broad selection of end-to-end analysis workflows, tools, and visualization modules, it enables easy and accurate discovery, verification, and validation of novel disease biomarkers.
Discover novel insights with greater than 95% sensitivity and unsurpassed accuracy. Biomedical Genomics Workbench guides you through a complete analysis of your genome, exome, targeted amplicon, transcriptome, and epigenetic NGS sequencing data for results you can trust.

  • Complete end-to-end and customizable analysis workflows for the comprehensive discovery, verification, and validation of novel biomarkers
  • Specialized functionalities such as primer and primer-dimer removal for highly accurate targeted amplicon sequencing results
  • High sensitivity detection of germline and low frequency variants from DNA-seq and RNA-seq data
  • Unsurpassed accuracy for copy number detection in exome and targeted amplicon sequencing data
  • Easy viewing of findings such as dynamic protein structures in 3D, and sequencing reads afford faster discovery