VA/VMRF Microarray & NGS Core

Roche 454 Squencing

  • Upgraded to GS FLX+ System
    • True capillary sequencing-like read lengths up to 1 kb
    • Flexible sequencing formats
    • Point-and-click data analysis
    • High-throughput sequencing for a wide range of applications
    • Designed for use with both the new long-read Sequencing Kit XL+ and existing Sequencing Kit XLR70
  • The Genome Sequencer FLX Instrument, powered by GS FLX Titanium and Standard series reagents, features a groundbreaking combination of long reads, exceptional accuracy and high throughput.
  • Applications: de novo sequencing, resequencing of whole genomes and target DNA regions, metagenomics and RNA analysis.
  • Generates more than 1,000,000 individual reads with improved Q20 read length of 400 bases per 10-hour instrument run. Combine long single reads and Long-Tag Paired end reads to completely assemble genomes, often within a single run.

Getting Started

  • Decide which sequencing application and read length best suits your needs
  • Library preps can be completed either by the user or by the Core
  • Contact us or Roche to determine amount of double-stranded DNA required
  • Download and fill out Sample Submission Form
  • Must have a valid PO number
  • Coordinate library drop-off via phone or email

Data Analysis

  • Once the raw sequencing data has been generated it will be run through Roche's 454 GS Run Processor. Changes to the default should be arranged prior to the completion of your run. All run files will be transferred to a flash drive provided by the user (please ensure enough storage memory is left on the drive).
  • Data is aggregated into 454 sequencing reads generating .sff and .fna files

Roche 454 Squencing

  • Parallel amplification of 48 targets from 48 samples, in effect generating 2304 sequencing-ready bar-coded amplicons, in just a few hours.
  • Libraries generated through this platform can be sequenced with Roche's 454 platform.
  • For one run of the 454, you can fit 8 Access Array Chips (8 Access Array Chips = 384 samples for one run of the 454).
  • 2 µl @ 50ng/µl are required per sample.


Genome Sequencer FLX System
Sequencing Run w/o Library Prep $6,647.06
1st Shotgun Library Prep $555.84
Additional Shotgun Library Prep $280.84
Amplicon Library Preps $305.84
1st Library Titration $748.18
Additional Library Titrations $523.18
Sequencing Run - Client provides GS kits & Library $805.00
Sequencing Run - Client provides GS kits and
enriched beads
1st Exome SeqCap - Client provides kits $400.00
Additional Exome SeqCap - Client provides kits $50.00


Fluidigm Access Array System
1 Run with 48 Samples and 48 Primers $1100.00


*Discount available for Cancer Center and DERC Members

*Non VA/UCSD users will be charged an additional 41.6% for Indirect Cost.