Whole Genome Sequencing Frequently Asked Questions

We provide raw data as FASTQ files for all projects. We also have advanced bioinformatics capabilities to provide optional data analysis services, including:

For resequencing of individual human genomes on Illumina platforms -

• Standard DNA Analysis Package: mapping, SNP/INDEL detection, structural variant analysis, and copy number variation detection
• De-novo assembly
• Tumor vs normal variant analysis
• Joint-genotyping
• Population genotyping
• Integration site prediction
• Custom analysis

For sequencing of non-human genomes on Illumina platforms –

• Standard DNA Analysis Package: mapping, SNP/INDEL detection, and structural variant analysis
• CNV discovery
• De-novo assembly
• Custom analysis

Larger structural variants can be better resolved with low coverage on long-read sequencing such as PacBio and Oxford Nanopore Technologies platforms. Complete to near-complete sequence assemblies can be obtained for most genomes.

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.

The turnaround time listed within the quote is inclusive of all steps quoted, unless otherwise noted. Timelines are based on first-pass processing. 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 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 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.

Initial sample QC can include: 

• Assessing RNA integrity by Fragment Analyzer and concentration by Qubit assay
  
• Assessing DNA concentration by Qubit assay and DNA size (for specific projects only) by pulse-field gel electrophoresis
• Assessing premade library size and concentration on the Fragment Analyzer and concentration by Qubit assay
• Assessing cryopreserved cells by cell counting and a cell viability assay
  

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 (e.g. Illumina MiSeq vs NovaSeq X Plus, PacBio Sequel IIe vs Revio, Oxford Nanopore GridION vs PromethION, etc.) 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 the GENEWIZ NGS team prior to project initiation.

You can contact the GENEWIZ NGS team at:

• US: NGS@azenta.com
• EU & UK: NGS.Europe@azenta.com

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 – at least X M CCS reads per Sequel IIe SMRT cell and Y M CCS reads per Revio SMRT cell. If a project does not meet these targets, an investigation will be conducted. If the issue is determined to be unrelated to the sample, a repeat or top-off will be performed as necessary.  

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

Delivery to most customer cloud solutions is free of charge. If you have any questions, please submit an inquiry.

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.

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.

For a quick tutorial, watch the video below.

For a quick tutorial, watch the video below.

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.