High Concordance between HiSeq 2000 and HiSeq 2500 Data

This new HiSeq® 2500 dataset, compares data quality and run time for a 2x100bp sequencing run on the HiSeq 2000 and the HiSeq 2500*. The HiSeq 2500 system maintains the industry-leading data quality of the HiSeq 2000, but delivers daily throughput in excess of 100Gb when used in rapid run mode.

Altogether, our sample-to-answer workflow takes around 50 hours for a 2x100bp 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.

HiSeq 2000 Run, HiSeq 2500 Run 1 (Flow Cell 1) and 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 (HiSeq 2500) or v3 kits (HiSeq 2000), PCR-free sample prep (in development), BWA/GATK analysis.

Summary of run

Summary of BWA/GATK alignment/variant calling

HiSeq 2000 vs 2500_blog_Final_Final

* Learn more about the features and specifications of the HiSeq 2500 system here. This is our third HiSeq 2500 dataset. View the “Genome in a Day” blog and dataset here. View the HiSeq 2x150bp blog and dataset here.

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

*** The total run on the HiSeq 2000 exceeded 600 Gb, but we focus on the yield of one of the samples for comparison purposes.

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About pierreturpin

Responsible for commercialization of on-premises systems for analysis of sequencing data at Illumina.

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  1. HiSeq 2500 Datasets now Available in BaseSpace | RNA-Seq Blog - December 4, 2012

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