Introducing fast, free alignment and variant calling with the Isaac Human Whole Genome Sequencing App

With the widespread adoption of the HiSeq 2500 and its lightning speed, enabling biologists to quickly and inexpensively extract biological information from sequences has become a critical need1,2. However, the management and analysis of large data sets is widely recognized as an obstacle to a wide adoption of next-generation sequencing, requiring large IT investment and bio-informatics expertise to set-up, maintain and run software at reasonable speed, especially for the most demanding applications like Whole Genome Sequencing (WGS).

To address this, Illumina has developed a user-friendly human WGS analysis workflow to enable scientists with no bioinformatics experience to align and call variants in whole human-genome data 4-6 times faster than existing methods. Combined with Illumina’s PCR-free sample preparation and the HiSeq 2500, the workflow provides a sample to answer time of less than 2 days.

In the words of Waibhav Tembe, Ph.D., Director of the Collaborative Bioinformatics Center at TGen “For whole genome sequencing, the aligner did an awesome job in cutting down the time to align 30x data against human genome and in using available hardware resources effectively.”

With the Isaac Human WGS app in BaseSpace, HiSeq users can now analyze and store WGS data without bioinformatics expertise, Linux experience or IT infrastructure. The workflow is free to use and can be accessed here (access requires a free BaseSpace account).

For those who prefer to keep their data on premises, the workflow is available as part of the HiSeq Analysis Software (HAS), freely available on the Illumina website here. HAS , can analyze WGS in a few hours, on a commodity PC with a single command line or an easy to use Graphical User Interface.

The component algorithms for the Isaac aligner and Variant Caller are released as open source here for developers to re-use and improve them. The open source version of the Isaac aligner is not commercially supported and provided as is under Illumina Open Source Software License available here.

Finally, data generated by Illumina’s IGN services uses the Isaac Human WGS workflow.

You can find more details on table 1 below and in our white paper available for download here.

Table 1: Isaac Human WGS workflow on premises with the HiSeq Analysis Software. Comparison of analysis metrics with the BWA + GATK workflow showing comparable data is generated 6 times faster.

(1)    Saunders, C. J. et al. (2012) Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units Sci Transl Med 4:154ra1352.

(2)    Jones, S. J. et al. (2010) Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 11, R82

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