Frequently asked questions about FastTrack sequencing services

Sequencing Service FAQs

Advances in genome sequencing technologies have enabled efficient characterization of the human genome, empowering researchers to better understand the underlying mechanisms of genetic disease.

Services provided by the Illumina FastTrack Services deliver a comprehensive analysis of the human whole genome.

Illumina FastTrack Services combines high-performance Illumina platforms with expert Illumina scientists; we deliver high-quality genotyping and sequencing data to support your research projects. You’ll reap the benefits of our Illumina technology, with a personalized service that delivers your data quickly and at a reasonable cost.

FastTrack Services offers a broad range of services, from whole-genome genotyping to custom content genotyping, and human whole-genome sequencing.

If you are interested in a project with Illumina FastTrack Services, please contact your sales representative or get a quote through our website. One of our sales representatives will discuss with you your sequencing project and help you to select the product that best fits your needs. Upon receipt of a quote, a project manager will contact you to discuss your sequencing project and the sample submission process.

For current turnaround times, please contact your local account manager, sales representative, or submit your question through our website.

The Illumina FastTrack Services offers a number of services. Depending on the service provided and the number of genomes, the price-per-genome varies. For current pricing information, please contact your local account manager, sales representative or get a quote through our website.

We require at least 2 μg of pure and intact DNA per sample. Please refer to the Sequencing Service Process for more information.

Once the FastTrack team receives your signed contract, you will be contacted by one of the project managers. The project manager is assigned to your project and will guide you throughout the process to adequately prepare and submit your samples to our lab. The project manager is responsible for tracking your samples though the lab and will be available throughout your project to answer any questions you might have about processes, samples, or deliverables.

We also have a team of scientific experts whose main priority is to ensure that every genome shipped is of the highest quality. They are available to discuss data integrity and provide technical expertise.

Samples are quantified upon arrival in our lab using Picogreen quantification. They proceed through library preparation in our Pre-PCR laboratory, then are transferred to the Post_PCR laboratory where the libraries go through clustering and sequencing. For more details on the lab workflow, please refer to the FastTrack Whole Genome Sequencing Service Methodologies.

The WGS analysis pipeline v3.0 employs Isaac Aligner, and Isaac Variant Caller to generate several outputs, including sequencing reads with reduced-resolution Q-scores in the BAM format, and variant data in both the VCF and genome VCF (gVCF)1 file format. The somatic small-variant calling component of the cancer analysis pipeline employs Isaac Aligner and Strelka2 to generate somatic small-variant data in the VCF format. These informatics pipelines enable significantly increased alignment efficiencies and reduced data footprints, without compromising the quality of the data and variant calls.

WGS sequencing analysis training packages and a cancer analysis training package are available in BaseSpace Sequence Hub, along with a Services user guideline and a quick video describing the deliverables. Please refer to Sequencing Services Training Material for more information.


Each of your samples is run in parallel on the HumanOmni2.5 genotyping chip. You will receive a file of the genotyped SNPs in a .vcf format that is outputted directly from the Illumina GenomeStudio software. These calls were obtained by applying the product standard cluster file to your data. For projects larger than 100 samples we recommend reclustering on the project samples, checking SNP performance, and re-exporting the genotype calls.

We will also provide you with intensity data files or IDATs files and a sample sheet. You can combine these files along with the product definition files (beadpool manifest .bpm, and standard cluster file .egt) found on Illumina’s support website to recreate a GenomeStudio project from the source data, allowing you to visualize and assess performance of the SNPs and samples.

Throughout our process customer samples go through multiple quality control steps and quality results are compared to internal controls for accuracy verification. QC is performed at each of the following steps: DNA quantification, post library prep, on-instrument sequencing and post genome build.

The FastTrack team performs downstream analysis (tertiary analysis) for our cancer analysis service offering.

Yes, Illumina FastTrack Services does offer a cancer analysis service for tumor-normal data set comparison. The standard offering is for a 40x normal and 80x tumor pair. Please refer to Sequencing Service Process for more information.

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