2x150bp Human Genome in Record Time with the HiSeq 2500

We are very happy to announce the BaseSpace availability of our second HiSeq 2500® dataset*. It demonstrates the ability to provide high quality 2x150bp reads in record time: 176 Gb in ~40h including on board cluster generation and sequencing, with 90.2% of bases at or above Q30, high quality alignment and variant calling.

Long reads allow a more precise analysis of gene fusions and structural variations, which have both been implicated in cancer and other diseases. Long reads also increase the quality of de novo assemblies based on metrics such as N50, contig size and genome coverage**. The incredible speed, daily throughput and data quality of the HiSeq 2500 is critical in settings where fast and accurate answers are required.

Altogether, our sample-to-analysis workflow takes around 50 hours for a 2x100bp run and around 74h for a 2x150bp run and we will soon commercialize methods to further improve this time.

Click on the links below to see the project and run folders. You will be asked to “Accept” the Run/Project into your BaseSpace account: this is the same mechanism you will use to share specific real-life projects or runs with your colleagues/collaborators via a dedicated URL.

Run 1 (Flow Cell 1), Run 2 (Flow Cell 2), Project (alignment and variant calling, analysis with App Store, file downloads)

Materials and Methods: Human Sample NA12878***, TruSeq Rapid SBS and Cluster Kits, PCR-free sample prep (in development), BWA/GATK analysis.

Summary of run

Summary of BWA/GATK alignment/variant calling


* Learn more about the features and specifications of the HiSeq 2500 system here  and see the first HiSeq 2500 “Genome in a Day” blog and dataset here.

** Benefits of Long, Paired-End Data for De Novo assembly are described in the Tech Note here

*** A member of the well-studied CEPH family. See details here.


    • Hi, the API on our developer portal will provide you with a way to write a program to get the data.

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