SeqCenter will be closed Saturday, December 21, 2024 through Wednesday, January 1, 2025 for Winter break. We will be unable to receive packages during this period. Two-week turnarounds will be offset by this closure. For full details on all TAT, shipping, and billing exceptions, please visit this page.

SARS-CoV-2 Sequencing

SeqCenter uses the latest set of primers (NEB VarSkip Short v2) to enrich your SARS-CoV-2 sample for viral reads. These primers, specifically designed to enhance coverage across Omicron variants, leverage a tiled amplicon approach. The resulting amplicons undergo sequencing via our standard whole genome sequencing pipeline, aiming for 150Mbps of reads per sample. This service includes assembling reads using the SARS-CoV-2 reference genome as a scaffold, and we provide both fastq and genome fasta files.

The ARTIC enrichment method effectively generates >70% coverage across genomes, even for samples with Ct values as high as 35. However, as we do not measure viral load before library preparation, we suggest using samples with Ct values below 35. We also accept raw samples in VTM media, which will be processed using Qiagen’s Viral RNA kits.

Sample Requirements:

  • Samples shipped frozen on dry ice
  • CT values <35
  • Total volume of:
    • 15 µL or more for purified RNA samples
    • 250 µL or more for samples submitted in VTM

What You Will Receive:

  • Fastq files (2 x 151bp) for each sample
  • Assembled SARS-CoV-2 genome
  • Sequencing stats summary
  • Materials and methods summary
  • Data shared via Globus within 2 weeks

Packages & Pricing

Sequencing Package
(Minimum Read Count Per Sample)		 Price*
Purified RNA $120.00
VTM Media
Requiring viral RNA extraction		 $135.00
*Orders >48 Samples receive 5% discount

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

Services:

About:

Resources:

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.

Go to Top