Iowa Institute of Human Genetics

  • Genome Sequencing

    Illumina HiSeq 2000/2500 Genome Sequencers

    Illumnia HiSeq 2000The IIHG Genomics Division currently operates the Illumina HiSeq 2000 and HiSeq 2500 genome sequencing platforms. Each instrument has 2 flow cells that each accommodates 8 sequencing lanes. The HiSeq 2500 has the ability to operate in 2 modes, High Output and Rapid mode, while the HiSeq 2000 operates in the High Output mode.

    The HiSeq instruments typically yield approximately 175 million reads per lane (range = 150 to 200 million reads). Since most applications require fewer reads, the IIHG Genomics Division can barcode (index) samples to permit the ability to load more than 1 sample per lane. Please contact the Division if you have questions about the depth of coverage needed for your project. Below are the HiSeq instrumentation run metrics.

    Performance Parameter High Output Mode Rapid Run Mode
    Read length (bp) 2x100 2x100 2x150
    Yield (Gb) ~600 ~120 ~180
    Run time ~11 days ~27 hours ~39 hours
    Bases>Q30 >80% >80% >75%
    Reads passing filter >90% >90% >90%
    Number of flow cells 2 2 2
    Lanes/flow Cell 8 2 2
    Cluster generation cBot Onboard Onboard

    Illumina MiSeq Seqencer

    Illumina MiSeqThe Illumina MiSeq is a “benchtop” version of the HiSeq instruments that uses a single lane flow cell capable of yielding 20 to 25 million reads per run. The run time ranges from 24 h (2 x 75 bp PE run) to 65 h (2 x 300 bp PE run) using the v3 sequencing chemistries. Typically 85% of the bases are greater than Q30 for 75 bp reads and are greater than 70% Q30 for 300 bp reads. This instrument is recommend for projects that require fast turn-around but do not require great numbers of reads.

    Life Technologies Personal Genome Machine

    Life Technologies PGMThe Genome Sequencing Service operates the Life Technologies Personal Genome Machine (Ion Torrent). This instrument provides the fastest sequencing runs that range from 2 to 7.5 h. This instrument is ideal for de novo sequencing of small genomes or projects that require fewer as listed in the table below. 

      Ion 314 Chip v2 Ion 316 Chip v2 Ion 319 Chip v2
    200 base
    400 base 
    30-50 Mb
    60-100 Mb
    300-600 Mb
    600 Mb-1 Gb
    600 MB-1 Gb
    Reads 400-550 Thousand 2-3 Million 4-5.5 Million
    Run Time
    200 base
    400 base 
    2.3 hours
    3.7 hours
    3.0 hours
    4.9 hours
    4.4 hours
    7.3 hours
    Research areas Cancer; Genetic diseases; Microbiology Stem Cell; Agriculture; Epigenomics Metagenomics; Forensic science; Ancient DNA genomics
    Key applications Targeted DNA sequencing; Copy number analysis; Targeted RNA sequencing; Small RNA sequencing de novo microbial sequencing; Bacterial typing; Viral typing; Metagenomics ChIP sequencing; Methylation analysis; SNP validation; Sequencing by genotyping
    • Learn more about the Ion PGM System