Technology:
The NCGR Sequencing Center operations utilize the Illumina HiSeq 2000, Illumina GAIIx, and Pacific BioSciences RS instruments. Genotyping operations are based on Illumina Infinium and GoldenGate chemistries using the iScan array scanner, supportd by Tecan robotics.

Certified Service Provider (CS-Pro):
NCGR is a CS-Pro for Illumina sequencing and genotyping services and also for the Agilent SureSelect target selection technology.

Sequencing Services:
The Sequencing Center offers sequencing, genotyping and target (exome) enrichment services providing high-quality results:

• Illumina DNA, RNA, ChIP and small RNA sequencing, mate-pair sequencing, and Pacific Biosciences long read sequencing.
• Sequencing of customer-supplied Illumina libraries.
• Sequencing for de novo transcript assembly.
• Illumina Infinium and GoldenGate genotyping.
• Agilent SureSelect target enrichment for sequencing customized genomic regions.

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Results:
Our expert staff was acknowledged by being the first Illumina CS-Pro service provider in North America and the first in the world to break the 20 billion base pair barrier using a single Illumina flowcell (January 2009). NCGR was awarded the Bio-IT World Best Practices in Basic Research for our schizophrenia studies using NGS for biomedical advancement, and the Computerworld Laureate award for our NGS analysis software.  Since then we have had premiere journal publications for our NGS and analysis work in research endeavors spanning diverse areas from animal and plant agricultural systems to human genetics.

Process:
Our experienced lab-operation staff manages a professional process:  disciplined scoping and scheduling of your project, SOPs and QC checkpoints, and deft handling of your samples from library prep through sequencing.  We then apply our unique NCGR contaminant filtering pipeline, producing the cleanest data results available.   Data is then delivered or additional informatics analysis commences (see Informatics Services below).

Analysis Services:
The Sequencing Center is tightly integrated with the NCGR Informatics group to bring customers professional analyses:

• Genomic SNP and Small Indel Discovery:  Alignment of genomic read data to a genomic reference to predict single nucleotide polymorphisms (SNPs) and indels.
• RNA-Seq Variant and/or Expression Analysis (using Genomic or Transcriptomic references):  Alignment of RNA-Seq data to a reference, prediction of SNPs and small indels, and read-count based expression and differential expression reports.
• De novo Transcript Assembly and Annotation:  De Bruijn graph based transcript assembly and annotation of protein products.

Our experienced lab-operation staff manages a professional process:  Disciplined scoping and scheduling of your project, SOPs and QC checkpoints, and deft handling of your samples from library prep through sequencing.  We then apply our NCGR contaminant filtering pipeline, producing the cleanest data results available. Data is then delivered or additional informatics analysis commences.