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Illumina DNA Sequencing

Illumina Whole Genome Sequencing Illumina Whole Exome Sequencing

Illumina is one of the leading short read Next Generation Sequencing (NGS) purveyors in the world, and their platforms underpin huge contributions to all fields of biological research since their introduction. Illumina platforms allow for massively paralleled sequencing that is adopted worldwide. The system relies on Illumina’s sequencing by synthesis (SBS) technology, where the addition of fluorescently-tagged nucleotides is optically tracked during DNA synthesis. With the highest per-base accuracy, the highest throughput, and competitively short run times, this platform has countless uses in both clinical and research applications.

While recent advances in sequencing technology bring huge increases in the data output of each run, not all projects need this increase nor can fill an entire flowcell. Through the use of barcodes, we multiplex samples on the same flowcell, providing economy of scale to even very small projects. We offer a core set of Illumina library preparations and sequencing pipelines but can also accommodate custom work by sequencing premade libraries incorporating Illumina’s standard sequencing adapters. For more information on all of our current Illumina offerings, please see below.

  • DNA Icon

    Illumina Whole Genome Sequencing

    Our Illumina Whole Genome Sequencing packages provide cost-effective short read sequencing using a tagmentation-based Illumina DNA library preparation. In addition to accommodating a wide range of sequencing size needs, this approach produces high-quality short reads suitable for a plethora of downstream analyses.

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  • Illumina Whole Exome Icon

    Illumina Whole Exome Sequencing

    Providing an economical alternative to WGS of the human genome, our whole exome sequencing approach focuses on sequencing the protein-coding regions. This approach utilizes a collection of panels to cover genes that are linked to phenotypes useful for biological, medical, and public health applications.

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Looking for sequencing without library prep? Our dedicated Illumina Full Flowcell sequencing services are designed for customers who prepare and pool their own sequencing libraries designed for an Illumina platform. Custom run structures are available for the dedicated flowcell options.

Illumina also powers many of our other pipelines for both DNA and RNA alike. Explore our other Illumina services for additional information.

Contact:
91 43rd Street, Ste. 250
Pittsburgh, PA 15201
(878) 227-4915

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Full Flowcell:

We offer full flowcell sequencing services for libraries that have been prepared outside of our lab. For each library, we will need to know the loading concentration, phiX spike-in, and run structure. Data is delivered as a complete run folder and can be demultiplexed upon request if a sample sheet is provided.

SARS-CoV-2 Sequencing:

Our SARS-CoV-2 Sequencing services include an assembly on the SARS-CoV-2 reference genome as a scaffold. These packages provide roughly 200Mbp of paired end reads (2×151 bp) as fastq files and the assembly in fasta format.

We require a minimum sample volume of 15 µL of extracted material (or 250µL for VTM samples) and recommend that only samples with Ct values below 35 are sent (because submissions are not measured for viral load before processing). We offer services for both purified RNA and samples in VTM media that require viral RNA extraction. Please see our SARS-CoV-2 Sequencing page for more detailed information.

Microbiome Sequencing:

Please see our Microbiome Sequencing page for package details, including distributables and sample requirements.

Nanopore Sequencing:

Our Oxford Nanopore sequencing packages provide reads equal to the length of input DNA, delivered as a fastq file.

For each sample, we require a minimum volume of 60 µL, and at least 40 ng/µL dsDNA quantified by Qubit or other dye-based method (100 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Long Read Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

PacBio:

Our PacBio services deliver HiFi reads with an average read length of 8-12kb for standard offerings and up to 25kb for full flowcell runs. All package names are listed by the minimum number of >Q20 reads that will be delivered. Both assembly and annotation are included with all packages.

For each sample, a minimum volume of 60 µL and at least 35 ng/µL dsDNA (quantified by Qubit or other dye-based methods) are required. SeqCenter strongly recommends utilizing our HMW DNA Extraction service for best results; however, we will also accept samples that are shipped on dry ice to avoid DNA integrity issues caused by the shipping process.

Please see our PacBio Sequencing page for more detailed information about our services.

RNA Sequencing:

We offer both rRNA depletion RNA squencing and polyA-tail enrichment mRNA sequencing. Both provide stranded, paired end reads (2x 151bp) as fastq files.

For each sample, we require a minimum volume of 20µL and at least 50ng/µL RNA. We also recommend, but do not require, that samples be DNAse treated and have a RIN score greater than 6. We also offer Basic and Intermediate RNAseq analyses, which require an annotated reference sequence.

Please see our RNA Sequencing page for more detailed information about both our RNA sequencing and analysis packages.

Illumina Sequencing:

The Illumina sequencing packages produce paired end reads (2×151 bp) delivered as fastq files.

For each sample, we require a minimum volume of 30 µL and at least 10 ng/µL dsDNA quantified by Qubit or other dye-based method (20 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Whole Genome Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

For additional information about variant calling and short read assemblies, please see our Bioinformatics page.

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