- Sequence Smarter / Illumina WGS
Illumina Short-read whole-genome sequencing
Illumina whole-genome sequencing for bacteria, fungi, viruses, and metagenomes. SeqCoast sequences 2×150 bp reads, provides expert review, and offers volume pricing from dozens to tens of thousands of samples.
SeqCoast provides high-throughput Illumina whole-genome sequencing for microbial isolates, phage and other viruses, mixed populations, and metagenomes. We run NextSeq 2000 and NovaSeq X platforms with X-LEAP chemistry to deliver 2×150 bp paired-end data for variant calling, assembly and annotation, antimicrobial resistance profiling, and comparative genomics, at batch sizes from dozens of samples to tens of thousands.
Why use Illumina short reads at SeqCoast?
Most widely used sequencing strategy, providing high read accuracy and high-throughput sequencing.
Our standard Illumina whole-genome sequencing services provide 2x150 bp paired reads.
We run projects from dozens of samples to tens of thousands, across NextSeq 2000 through NovaSeq X.
We use modern X-LEAP chemistry for high read accuracy and high output per run.
Short-read whole-genome sequencing applications
Example microbial sequencing targets:
-
Microbial isolates:
- Bacteria
- Fungi (yeast, filamentous)
- Single-cell eukaryotes (e.g. algae, amoeba)
- DNA phage or other viruses
- Whole populations (e.g. experimental evolution, intrastrain diversity)
- Metagenomes (e.g. microbiome, soil, contrived communities, wastewater)
Example applications where short reads shine
- Reference-based variant calling for clones or populations
- Assembly and annotation
-
Pathogen profiling
- Antimicrobial resistance (AMR)
- Surveillance
- Plasmid detection and identification
- Virulence factor characterization
- MLST and intrastrain relatedness
- Longitudinal analysis
-
Metagenomic profiling
- Relative abundance
- Diversity statistics
- AMR
SeqCoast features and benefits
Our expertise and high-throughput capabilities make us the ideal partner for custom projects of any size or complexity, whether you have dozens or thousands of samples.
Flexibility at scale
- High-throughput sequencing, with capacity to process hundreds of thousands of samples.
- Data volumes ranging from 200 Mbp to 50 Gbp+ per sample.
Gold-standard library preparation and sequencing
- Illumina library prep and sequencing reagents – no off-brands, homemade reagents, or compromised quality.
- Robust, tagmentation-based library preparation that can effectively handle a wide range of GC contents.
- Exclusive use of unique dual indexes (UDIs) to prevent index hopping.
- High read accuracy (Q30+) and high throughput.
Multi-point QC
- All samples checked upon arrival to ensure they have arrived intact and conform to biosafety standards.
- Library concentrations are measured to ensure appropriate library pool balancing and optimize data output for each sample.
- Sequencing quality metrics checked by a qualified expert.
- Custom QC services available upon request for large orders.
Need custom analysis?
Most projects are covered by our standard analysis pipelines above. If your project requires custom analysis, tell us about your project goals and needs!
How to prep samples for submission
Send raw samples
- Send raw samples for our robust DNA extraction workflow.
Or send purified DNA
- Send >10ng/ul of DNA in a volume of >20ul eluted in nuclease-free water or dilute TE.
- We accept samples that have lower concentrations/volumes, but they may have a lower chance of success.
Quantification and elution
- We strongly recommend quantifying by Qubit or other fluorometric method, as other methods (such as Nanodrop or Tapestation) are often wildly inaccurate.
- We recommend eluting samples in nuclease-free water or diluted TE, but we do accept other elution buffers.
- Excessive EDTA and extraction contaminants (salts, phenol, polysaccharides, etc.) can cause sample failure.
48+ samples
- We offer our COMPASS system for CoOrdinated Management and Processing for Accelerated Sequencing Services.
- COMPASS allows for the fastest processing and the lowest price!
- You will receive a custom shipping container with validated plasticware, stabilization buffer, & prepaid shipping label at no additional charge.
24-48 samples
- Must be sent in a 96-well plate or individually-capped 8-tube strips.
- 96-well plates should be fully-skirted and sealed well with a foil seal (plastic seals are very prone to leaking during shipping).
<24 samples
- Individually-capped 8-tube strips (preferred) or 1.5 mL tubes.
96-well plates
- Label with Order Number and (if necessary) Plate Number.
Tubes
- Label caps with SeqCoast Sample ID (assigned in your Sample Manifest).
- Labeling tubes with your own sample names instead of the SeqCoast Sample IDs can cause delays!
Please send
All samples must be securely packaged in a clean, organized fashion using secondary containment. Leaking samples will be immediately disposed of, as required by our biosafety measures.
Please do not send
Bags of tubes, individual tubes wrapped in parafilm, large-format tubes (e.g. 50ml conicals), non-sterile/soft-sided containers (e.g. plastic bags), unsealed cell culture 96- well plates. We’ve seen it all! Please double-check your shipments to ensure your samples make it to us safe and sound.
Data delivery, security, and access
We make it easy to access your data!
Most Illumina orders are completed within 10 business days of sample receipt.
Data delivery options include SFTP Download, AWS transfer, Box.com, and alternatives on request.
Data are stored on AWS cloud infrastructure in the United States, providing scalable storage, high availability, and industry-recognized security controls.
Pricing — the more you order, the lower the price!
How much sequencing data do I need for Illumina sequencing?
If you are unsure about the data volume per sample you need, we recommend that you do one of the following:
- Perform a literature search for similar sample types and analyses.
- Send pilot samples aiming for more data than you think you need, then use down-sampling methods to determine the optimal data volume for your full experiment.
While we do not provide specific recommendations for every project, please see the following table for illustrative examples of data volume tiers that our customers have used:
- To make a draft quality assembly (dozens or more contigs): >30X Illumina short reads
- To make a reference quality assembly: Purchase one of our hybrid bundles to leverage the quality of short read sequencing with the read lengths of long read sequencing.
- Clones: >30X coverage
- Populations: >100X coverage, deeper sequencing is needed to detect rare alleles
- >40X coverage Illumina sequencing recommended
- Human gut microbiome — 10 Gbp
- Wastewater — 1–5 Gbp
Frequently Asked Questions
How should I extract my DNA?
Let us do the hard work for you! We offer DNA extraction using bead beating lysis.
If you want to tackle it yourself, many column-based extraction kits provide good results, as do other methods if care is taken to remove contaminants. Our library prep methods work best with buffers containing less than 1mM EDTA.
Can I send a lower concentration or volume than your recommendations?
Yes, we are often successful with lower-concentration samples and are happy to process any samples that you send!
Please note that samples that do not meet our recommendations have a lower chance of success.
Custom low-input library preparation services are available for large orders.
How much data should I order?
See the “How much sequencing data do I need for Illumina sequencing?” section above.
Is the library preparation tagmentation-based or ligation-based?
Our standard Illumina library preparation is tagmentation-based and uses gold-standard reagents from Illumina.
Do you perform sequencing for phage and other viruses?
Our standard Illumina service is compatible with dsDNA phages and other dsDNA viruses!
For these samples, we recommend our “Illumina; 200 Mbp/1.3 million reads” service.
If your viral genome is linear, coverage will be greatly reduced for the distal 50bp regions due to the tagementation-based library prep approach. You can use our ligation-based Nanopore sequencing workflow to circumvent this issue!
Do you have requirements for A260/230 and A260/280 absorbance ratios?
Our library preparation workflows are generally quite robust and can tolerate moderate deviations from ideal absorbance ratios.
We do not have requirements surrounding absorbance ratios and will not provide recommendations on whether your ratios are sufficient.
However, please be aware that lower-quality samples have lower chances of success and may require that you perform a cleanup prior to sending them for sequencing.