Sequencing Only FAQs

We offer high-throughput next generation sequencing (NGS) on pre-made NGS libraries using Illumina® platforms.

You can submit any Illumina®-compatible library for sequencing. If the library preparation used Illumina® adapters during ligation, these will be successfully sequenced using GENEWIZ’s Sequencing Only service.

You can submit libraries up to 600 bp.

Yes, we offer next generation sequencing of pre-made NGS libraries on other NGS platforms, including long-read platforms. Please contact the team by submitting an inquiry.

Yes, please instruct our team what percentage of PhiX spike-in to use, and we’ll accommodate the request free of charge. See the following recommendations of PhiX spike-in:

• ~20% taxon identification (ITS/16S/18S) and WGBS
• ~30% amplicon and small RNA libraries
• ~5%-10% low diversity libraries

Please indicate that you require data analysis upon submitting your instant quote.

Yes, please indicate that your libraries have custom sequencing or index primers upon submitting your instant quote.

There are several Illumina® sequencing configurations available including 2×150 bp, 2×250 bp, 2×300 bp, and 10x sequencing.

GENEWIZ has a variety of sequencers, offering different amounts of data output:

• 2×150 bp configuration: MiSeq flow cell (4.5 Gb), NovaSeq X Plus 10B flow cell (3,000 Gb), NovaSeq X Plus 25B lane (950 Gb), NovaSeq X Plus 25B flow cell (7,600 Gb)
• 2×250 bp configuration: MiSeq flow cell (7.5 Gb), NovaSeq 6000 SP flow cell (325-400 Gb)
• 2×300 bp configuration: MiSeq flow cell (13 Gb)
• 10x sequencing only: NovaSeq X Plus 25B lane (950 Gb), NovaSeq X Plus 25B flow cell (7,600 Gb)

A flow cell is a glass or polymer slide used in NGS platforms (like Illumina®) where DNA fragments are immobilized, amplified, and sequenced. It contains multiple lanes or channels that can be loaded with different DNA libraries.

A dedicated lane/flow cell means ordering and utilizing the entire lane of a flow cell or the entire flow cell. The lane/flow cell is dedicated to your individual project, maximizing throughput and minimizing cross-contamination risk.

A partial lane/flow cell refers to using only a subset of the lane of a flow cell. The remaining lanes may be used for other projects or pooled with other users’ samples. This is often called lane sharing or multiplexing across lanes. This option is only available for 2×150 bp configuration.

There are several data packages available: 105 Gb, 375 Gb. The data package will be assigned based on the total number of libraries, amount of data per library, and amount of PhiX spike-in required.

• Large-scale projects needing high read depth
• Clinical or regulatory-grade sequencing where contamination must be avoided
• Require sequencing configuration outside of 2×150 bp (i.e. 2×250 bp, 2×300 bp)
• Require specific Illumina sequencing platform to keep continuity for publication purposes

• Smaller projects with fewer samples needing less than 950 Gb of data output
• Cost-conscious sequencing where full lane/flow cell capacity isn’t needed
• Sequencing configuration of 2×150 bp

The risk is minimal, but possible. GENEWIZ has an optimized and efficient process of pooling samples from different projects to ensure the highest quality and chain of custody.

Yes, the sequencing chemistry remains the same. The difference lies in how the lane/flow cell is allocated and utilized.

Please submit a quote request to receive accurate pricing information, as the cost depends on the details of the project. Please submit an inquiry to inquire about your specific project needs.

Partial lane/flow cell runs are less total money because you pay for a smaller data package. Dedicated lane/flow cell runs are more expensive but more cost-effective by cost per Gb.

Illumina®-compatible libraries require four major components in their adapter sequences, found at the ends of each fragment, for paired-end sequencing:

• Flow cell binding sites. Known as P5 or P7, they facilitate clustering of the DNA strands on the flow cell.
• Sequencing primer binding sites. Labeled as Read 1 and Read 2, they are necessary to initiate sequencing at both ends of the fragment.
• Index sequences. Often called i5 and i7, they act as barcodes to allow multiplexing (pooling) of samples. Libraries can be either single index (having one index sequencing) or dual index (having two index sequences), and each library to be pooled requires at least one unique index.
• Index primer binding site(s). These are required to read the index sequences.

The composition of the adapter sequences depends on whether the library is single or dual indexed (see figure below). If any of the components are missing, heavily modified, or in the wrong configuration, sequencing may fail. If you have any questions regarding your library configuration, please contact us.

Single-Indexed Sequencing

Dual-Indexed Sequencing

Please indicate what type of indexed sequences (index primer binding sites) your pre-made libraries contain upon submitting your instant quote.

GENEWIZ can accept sequencing libraries with index configurations of 6 bp (most single index applications), 8 bp (most dual index applications), 10 bp, and 16 bp. Other custom index options are available. Please submit an inquiry for more details.

Yes, we will provide the de-multiplexing step free of charge. We ask that you provide the index sequences in the Sample Submission Form prior to your sequencing run.

The GENEWIZ NGS Team is composed of Ph.D. scientists who can help you optimize your project design and provide consultation. You can contact the team by submitting an inquiry.

Our team prioritizes fast turnaround times and provide a timeline based on first-pass processing. The turnaround time listed within the quote is inclusive of all steps quoted, unless otherwise noted. If repeat processing is required, the turnaround may be subject to change and will be proactively communicated to the client.

If the scope of a project changes after project initiation or if sample or project clarification is required after sample receipt, GENEWIZ may reassess the turnaround time based on the subsequent communications and modifications (if applicable).

All extraction kits and reagents are routinely updated to remain best-in-class. Please proactively contact GENEWIZ if you would like historical versions, which may be available on a case-by-case basis.

Extractions are performed to the best of our ability and are unable to guarantee yield due to multiple variables that may affect sample yield and quality. Costs to cover the work performed will be applied, regardless of the outcome.

All library kits and reagents are routinely updated to remain best-in-class. Please proactively contact GENEWIZ if you would like historical versions, which may be available on a case-by-case basis.

For most of the services, an initial sample QC is included within the fee of the project for all samples that will proceed to the next processing stage (e.g. library preparation or sequencing) unless otherwise noted within the quotation. Resubmissions or additional, optional samples may incur a nominal fee for QC.

Most services include an initial sample QC within the project fee for samples proceeding to the next stage (e.g., library preparation or sequencing). Resubmissions or additional samples may incur a small QC fee unless noted otherwise in the quotation.

Initial sample QC can include:

• Assessing RNA concentration and integrity
• Assessing DNA concentration and DNA size (for select projects)
• Assessing premade library size and concentration
 
• Assessing cryopreserved cells by cell count and viability

The sequencing platform will be listed within the Service Description of the quotation.

Unless specifically noted in the quotation, GENEWIZ reserves the right to choose between equivalent instruments depending on the target read depth and configuration requested. If a specific instrument is required, please add special comments in your quote/order and notify our NGS team prior to project initiation.

Illumina-based projects

For samples that pass QC and libraries prepared at GENEWIZ:

Data Quality

• NovaSeq 2x150bp: ≥85% of bases ≥Q30
• NovaSeq 2x250bp: ≥80% of bases ≥Q30
• MiSeq 2x150bp: ≥80% of bases ≥Q30
• MiSeq 2x250bp: ≥75% of bases ≥Q30

Data Yield

• Within 10% of total data target yield per lane or flowcell, unless otherwise noted
• Within 20% of per sample target yield, unless otherwise noted

Quality and yield for samples that do not pass QC and are processed at best effort are not guaranteed. Premade libraries/library pools submitted for sequencing only quality and yield are evaluated on a case-by-case basis.

Multiplexing is performed to the best of our ability to ensure relatively even data distribution amongst samples.

PacBio-based projects

Due to various sample-related factors that may influence long-read sequencing yield and quality, GENEWIZ cannot guarantee overall data output and quality. However, based on extensive experience with long-read workflows, GENEWIZ has established target metrics based on the PacBio system based on the sample submitted and library type. If a project does not meet these targets, a thorough review of the processing will be performed. If the issue is determined to be unrelated to the sample, a repeat or top-off will be performed as necessary.

Due to the possible wide range of performance being influenced by sequence complexity and sample quality, GENEWIZ does not guarantee average coverage or on-target specificity for each sample. We can instead recommend target data output that would increase the chances of obtaining the desired coverage based on the sample and library type utilized.

Data analysis is performed to the best of our ability and results are not guaranteed for samples or libraries not passing QC or do not fit the analysis pipeline’s criteria.

Yes, we can recommend the best data delivery option based on the platform and project details. Options include:

• Secure File Transfer Protocol (sFTP) – additional charges may apply
• Customer Cloud Account – AWS, Microsoft Azure, Google Cloud
• Hard Drive – additional charges may apply

By default, results are sent via a secure File Transfer Protocol (sFTP). Please refer to our sFTP Data Download Guide for instructions on how to download your data and troubleshooting tips. Additional charges may be applicable for large data transfers.

Please refer to the delivery email sent from GENEWIZ for detailed information on the transfer and consult with your IT department to ensure compliance with your institution’s policies.

We take data security very seriously and we make every attempt to keep your data private and protected. The data transfer we offer is secure; however, should you desire an alternative delivery method, we are happy to work with you.

We hold any remaining samples for up to 3 months after project completion. Clinical samples processed in our Regulatory-Environment or CLIA-licensed laboratory may have longer sample storage timelines. Please contact us if you would like samples retained for a longer period or shipped back to you.

GENEWIZ offers raw data storage (i.e. FASTQ for Illumina, BAM for PacBio, POD5 for Oxford Nanopore) for up to 6 months after project completion. Data generated for samples processed in the Regulatory-Environment or CLIA-licensed laboratory may have longer data retention timelines. Please contact us if you would like the data to be retained for a longer period. 

View our Sample Submission Guidelines for instructions on preparing and sending samples. Organize your samples in tubes or plates following the order indicated on the sample submission form.

• Tubes: Prepare samples in clearly labeled and well-organized 1.5 mL flip-cap microcentrifuge tubes. Please avoid using Parafilm to seal the tubes.

Unless otherwise instructed, GENEWIZ reserves the right to combine multiple vials of the same sample for extraction and/or library preparation.

• Plates: For projects with 16 or more samples, prepare samples in clearly labeled, securely sealed 96-well full-skirted PCR v-bottom plates. Arrange the samples vertically by column (i.e. A1, B1, C1, etc.)

Ship samples directly to our facility. Use the shipping address listed on the order receipt.

Please reach out to us by submitting an inquiry.

Request a quote through your GENEWIZ account. Click on the service you’d like to order.

Log into your GENEWIZ account to confirm your quote.

The status of your order, including an estimated date of delivery, can be viewed anytime through your GENEWIZ account. Visit the Order Summary page of your project to find the current order status.

Option #1: Ship samples directly to our facility. Use the shipping address listed on your order receipt.

Option #2: For double-stranded DNA samples, submit samples into a local GENEWIZ dropbox which are conveniently located throughout the US, Europe and United Kingdom. To locate a dropbox near you, please submit an inquiry. Place your order receipt and samples in a Ziploc bag packaged according to sample submission guidelines specific for your Next Generation Sequencing service. 

Note: Not recommended for RNA and primary sample types. 

During checkout, consult the Order Summary page to find out the daily cutoff times for your selected dropbox (see example below).

If you miss the dropbox deadline, feel free to ship samples directly to us.