The HudsonAlpha Genome Sequencing Center is constantly improving its technology and knowledge base to keep current with the rapidly advancing sequencing technologies. Some of its sequencing technologies include:

PacBio long read sequencing

PacBio Sequel II and Sequel IIe
The PacBio Sequel II and Sequel IIe system uses Single Molecule Real-Time (SMRT) sequencing to provide a direct real-time readout of each base from single DNA molecules. The SMRT technology uses one million microwells bound with a DNA polymerase (zero-mode waveguides (ZMW)) to capture signal from the incorporation of fluorescent-labeled nucleotides during DNA replication of SMRTbell templates. The detection system records a movie of light pulses that are converted to base calls to create a continuous long read from each ZMW.


  • Long reads- tens of kilobases in length
  • High accuracy- >99.999% consensus accuracy
  • Uniform coverage- No bias based on GC content
  • Single-molecule resolution
  • Reads the same molecule multiple times for high consensus accuracy
  • Deeper biological insights, less data processing, and faster results thanks to the unmatched clarity of HiFi reads
  • Reliable and affordable high-throughput sequencing for a broad range of applications
  • Gain insight into difficult to sequence regions of the genome
  • Better data for superior results with lower coverage, from a single technology
  • Less time spent on data processing and analysis for faster answers
  • Cost savings at every step of your sequencing pipeline

Sequencing Applications:

  • De novo sequencing
  • Variant detection
  • Complex populations
  • RNA sequencing
  • Epigenetics
  • Targeted sequencing

Check out this video to hear HudsonAlpha Genome Sequencing Center co-director Jeremy Schmutz discuss the benefits that HiFi reads from the PacBio Sequel II System bring to sequencing, assembly, and analysis of complex genomes.

The HudsonAlpha Genome Sequencing Center were beta testers for the PacBio Sequel II system in early 2019. Today we operate seven Sequel II systems (Sequel II and Sequel IIe) and are one of the world’s largest SMRT Sequencing facilities. Learn More →

Illumina short read sequencing

NovaSeq 6000
The NovaSeq 6000 system detects unique fluorescence from clonally amplified DNA templates. The patterned flow cells have a defined, organized array of etched wells that each contain a DNA probe for adhering complementary sequences added to DNA libraries. This patterned flow cell replaces the randomly scattered clusters found in imaging intensive, non-patterned flow cells responsible for slower processing time. By providing multiple flow cell types and read lengths, the NovaSeq can accommodate a variety of sequencing methods, project scales, and data needs.


  • High-throughput sequencing
  • Patterned flow cells with scalable throughputs to accommodate most projects
  • Maximum output per run- 6 Tb
  • Maximum reads per run- 20 billion
  • Simple streamlined automated workflows
  • Configure the system to sequence a trio in one day or up to 48 genomes in ~2 days for the most comprehensive coverage

Sequencing applications:

  • Large scale resequencing of humans, plants and animals
  • Transcriptome sequencing
  • Hi-C sequencing
  • Amplicon sequencing


MiSeq is a benchtop sequencer specializing for quick, lower-output runs on single-lane flow cells, and offers Illumina’s longest read length – the 300-bp paired-end run. Ideal for projects requiring 1- 16 million reads/run.


  • 3 trillion bps per day
  • Targeted gene sequencing 1.2 Gb Max output per run
  • Maximum read length 2 X 150 bp, 4 million reads per run
  • Patterned flow cell technology
  • Fast sequencing turnaround while maintaining high data quality
  • Flexible system with a wide range of applications

Sequencing applications:

  • Whole genome sequencing of small viral or microbial genomes
  • Targeted gene sequencing

Sequencing Assembling and Analysis

De novo Genome Assembly
The HudsonAlpha Genome Sequencing Center is one of the few centers in the world performing original sequencing of plants and animals. The non-profit center has generated and publicly released reference genomes for more than 180 plants. Reference genomes serve as a point of comparison for future study and lay the foundation for downstream functional studies for the improvement and production of domesticated crops. In the cases of crop species such as sorghum, soybean, cotton, switchgrass and millet, these genomic references form the basis for genomics-enabled crop breeding to increase yields.

Genome Sequencing Analysis
Advanced technologies have given us both access to complex plant genomes and the ability to examine genetic differences across thousands of plant varieties. In addition, high performance computing allows us to analyze and integrate these enormous amounts of data.

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