The CoreMarketplace: Next Gen Sequencing and Analysis Center

National Center for Genome Resources

2935 Rodeo Park Drive East

Santa Fe, NM 87505

http://www.ncgr.org

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Primary Contact:

Faye Schilkey

Last Updated: 11/17/2010

Facility Details

Genome Sequencing Center
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SEQUENCING
o Illumina Certified Service Provider (1st in North America)
o Illumina GAIIx & HiSeq2000, SOLiD, PacBio RS
o Whole Genome/Transcriptome Shotgun, mRNA Seq,
ChIP-seq, small RNA
o Singleton and mate-paired reads

TARGET SELECTION
o Enrich subsets of genes and other selected regions using NimbleGen, Agilent or Raindance technologies

INFORMATICS
o Genome/Transcriptome Analysis
o Alpheus® cloud-based analysis system for sequencing data (http://alpheus.ncgr.org/)
o Nucleotide variant, in/dels, premature stop codons, splice isoforms, genomic rearrangements, and expression detection
o JMP-Genomics expertise and interface for downstream statistical analysis
o Custom Assembly/Annotation services

GENOTYPING
o Illumina-based genotyping assay for human, plants and animals

Sequencing infrastructure: Cluster stations for flow cell construction, and Agilent bioanalyzer, NanoDrop, PicoGreen devices for sequencing library quantification QA/QC. The wet lab has a full compliment of molecular laboratory equipment (e.g. ultra-low , -20 and 4 oC temperature freezers, centrifuges, agarose gel electrophoresis and gel documentation equipment) to support up to four workstations/researchers.

IT Infrastructure:
Data Storage (file servers)
- Four Sun X4500 - 24 TB (96TB total)
- One Sun X4540 48TB
- Isilon cluster 144TB
Image processing/Basecalling
- Two Sun X4150 and and one x4170 Total: 6 x - 4-core processors, 24 GB RAM, 12 x 146GB Hard drives
Variant detection
- 10 Sun Blade 6000 chassis with 100 x 6220 Blades (600 Cores, 2TB of RAM and 58.4 TB disk)
DB storage
- Two sun 4150, two 4450 DB Servers, 6140 SAN with 70 TB for DB disk space, 4 Gb/s Switch fabric

Other Facility Information

Alpheus® Next Generation Sequence Data Analysis: Analyzes high-throughput, low-cost next generation sequencing data (Illumina-Solexa, Roche-454, ABI-SOLiD) with characteristically short reads is problematic for conventional assembly and analysis pipelines. The Alpheus software system identifies variants (i.e. SNPs or indels) in these short reads and filters them based on consistency, allele frequency, quality, coverage, and variant type to reduce false positives. Alpheus also determines gene expression, comparing values across groups of samples. Alpheus features automated data handling, a computational analysis pipeline, a relational database and a web-based query and visualization interface allowing researchers secure access via any web browser.