FAQs

The Library Prep Kit for myBaits is designed for input amounts from 1 to 500 ng. Please see the kit manual for technical recommendations.

Please see the kit manual for detailed technical recommendations on the enzymatic fragmentation step. In brief, the final length of your DNA after fragmentation will depend on the (1) the length of your starting genomic DNA sample and (2) your chosen fragmentation time.

myBaits hybridization capture can tolerate NGS library insert lengths from 50bp-10Kbp. However for most myBaits applications, users should aim to generate NGS libraries with ~300-500bp length inserts (~450-650bp length libraries).

Yes, the Library Preparation Kit for myBaits is compatible with a wide range of input DNA qualities, from high-molecular weight to highly degraded.

However, some degraded sample types (such as formalin-fixed, ancient DNA, and others) may have chemical modifications, crosslinking, sequence breaks, or other types of damage that can restrict the conversion those DNA molecules into a functional NGS library. In order to be compatible with this Library Prep Kit, the target DNA molecules must be double-stranded and able to be enzymatically end-polished and adenylated (A/T overhang) to enable ligation of the sequencing adapters.

Regardless, the enzymatic fragmentation outcome will be affected by the starting length of your DNA samples. Please see the kit manual for technical recommendations for selecting the correct fragmentation approach for your project goals. In brief, the final length of DNA after fragmentation will depend on the (1) length of starting genomic DNA and (2) the chosen fragmentation time.

Yes! From our team of experts, we offer comprehensive NGS laboratory and bioinformatic services appropriate for a wide range of sample types. We offer flexible services including DNA/RNA extraction, NGS library preparation, myBaits capture, short- or long-read sequencing, and/or bioinformatic analysis.

All of Arbor’s library preparation service options are AVITI-compatible.

Please see the library kit compatibility guide from Element Biosciences for a list of kits with which AVITI sequencing is compatible.

Briefly, compared to the figure below, the 5’ and 3’ end of the adapters must not have missing, additional, or mismatched bases or modifications that would block DNA ligation:

Yes! A full AVITI flowcell generates approximately 240Gbp of PE150 data.

If you need more data and need it speedily, the AVITI can run two flowcells simultaneously.

Yes! We can offer AVITI sequencing in units of Gbp, which is ~3.3M PE150 read pairs. The price per Gbp goes down the more Gbp you get!

You’ll receive demultiplexed, but otherwise raw FASTQ files. There will be two files (read 1 and read 2) per sample. If you are familiar with Illumina sequencing output, the data will be identical to the format you are familiar with.

• Decreased sequencing turnaround time. With the sequencer in Arbor’s hands, we’re in full control of the speed and can provide data at least 2 weeks faster than ever before.
• Increased read quality. Runs frequently produce results with >90% of reads meeting or exceeding Q30 quality scores. 
• Flexibility. Mid-sized flowcells (~240Gbp) make flowcell-level pricing accessible for smaller project sizes.
• Compatibility. The AVITI is compatible with all of Arbor’s existing short-read library preparation (and capture) options, so you can feel confident knowing that your precious samples will be handled with the protocols you trust. 

While the output (FASTQ files) is the same, the sequencing chemistry is different. The AVITI uses “avidity sequencing,” which is a sequencing-by binding chemistry. Illumina sequencing employs a sequencing-by synthesis chemistry. The avidity sequencing chemistry improves the accuracy of the basecalls. Read more about avidity sequencing here.

AVITI is the new short-read medium-throughput sequencing platform from Element Biosciences. It is a drop-in replacement for Illumina sequencers – meaning that it is compatible with Illumina libraries and the data format is the same as you’d get with an Illumina sequencer.

Many sample types and species will require special permits for shipping internationally (or domestically). We can provide some advice, but ultimately you are responsible for proactively identifying the permit(s) that are required for your unique samples. Some examples of biological samples that require permits are tissue or DNA from CITES-listed specimens and plant tissues regulated by the USDA/APHIS.

If Daicel Arbor Biosciences is required to apply for an import permit on your behalf, you will be required to pay a permit application fee, regardless of whether the application is successful.

We strongly encourage our customers to research shipping regulations before contacting us about your project to determine your specific permit needs. Incorrect or incomplete documentation may result in the seizure and loss of your samples at Customs, and potentially the assignment of fines/fees.

Yes. We require documentation that all relevant and necessary ethics approvals have been granted for any human specimens that you would like us to work on. This includes both contemporary and ancient samples and includes both tissue and nucleic acid derivatives. Please contact us to receive our Ethics Statement document if you are interested in sending human samples to us. We do not accept clinical specimens and are not CLIA-certified.

We prepare short-insert libraries with 8-bp unique dual indexes.

We prepare long-insert libraries with 16 bp identical dual indexes.

Our library preparation protocols have been carefully tested and optimized for both WGS and targeted sequencing applications. We have protocols that are appropriate for a wide range and variety of input qualities and quantities that have been successfully applied to thousands of samples. Therefore it is very likely that one of our existing protocols will work well for your application, but if you have very specific project constraints, our NGS experts would be happy to discuss the options with you.

Upon arrival, we will take a look at your shipment and plastics to ensure that the samples have not been damaged during their journey. At that point, your project will enter our QC queue.

For Standard and Long Insert quality DNA samples, we will quantify the total gDNA with a spectrofluorometric assay, purify up to 80% of the material, and re-quantify the samples. For Degraded quality DNA samples, we will perform the initial total gDNA quantification as well as visualize at minimum a subset of your samples on the Agilent TapeStation platform. For Ancient quality DNA samples, we will perform the initial total gDNA quantification and may visualize a subset of your samples on the Agilent TapeStation platform.

For RNA samples, we will perform a total RNA quantification. If you have ordered our RNA clean-up, we will perform a DNase treatment, a bead-based purification, a visualization via Agilent TapeStation, and a second total RNA quantification.

For pre-made libraries, we will perform a total gDNA quantification as well as a qPCR-based assay for properly adapted Illumina-compatible library molecules.

If you order QC-only services, the “Standard QC” is the same as the Standard DNA quality QC above. The “Extended QC” is the same as the Degraded DNA quality QC.

We will provide a QC report with the results of our QC to you when you send us DNA, RNA, or libraries. We will also perform the appropriate QC and send the QC report for samples for which we perform the DNA/RNA extraction.

Yes. You can order our “Degraded DNA Package” if you would like our full service package or “Extended QC” if you would like a custom project configuration and we will evaluate the quantity and the quality of your samples. You will be provided with a QC report and our NGS experts are available to consult with you about the results and can suggest some options for moving forward with your project.

Yes. We are able to expedite a select number of projects at a given time. Please inquire if you believe your project needs to be expedited and we will let you know if we have availability in our expedited pipeline and if the desired project timeline is feasible. When a project is expedited, it will skip our regular queue. We do not guarantee a specific turnaround time guarantee for expedited projects. We will do our best to be transparent with anticipated timelines and will communicate progress as well as delays with you during the process.

Yes. Please do your best to provide your project information as accurately as possible and we would be happy to provide a price estimate for you to use in your grant proposal. However, please be aware that our prices may change between when your estimate is provided and when your grant is funded.

We pride ourselves on our professionalism, which goes beyond technical expertise. We have a team of highly skilled bioinformatics experts with years of experience in NGS data analysis, ensuring the accuracy and reliability of your results and we emphasize clear and regular communication, proper planning, and execution to ensure the best possible collaboration and experience for our clients. We offer a comprehensive suite of bioinformatics services and strive to be flexible by providing personalized service tailored to your specific needs and preference. We use state-of-the-art software and computing resources to ensure that your NGS data is processed quickly and accurately. Additionally, our commitment to excellent customer service and support is unwavering throughout the entire process. We are always available to answer questions, provide guidance, and work closely with our clients to ensure the success of their projects.

The pricing of our bioinformatics services depends on the specific requirements of your project. Once you contact us, we will provide no-charge project consultation upfront to assess your needs and determine a detailed project plan, after which we can quickly provide you with a detailed quote.

The custom bioinformatics service process begins with a consultation to understand your research goals and project requirements. Our team of experts then provides tailored solutions, including customized data analysis pipelines, software development, and consulting services, to meet your specific needs. The final results are delivered in a timely and reliable manner, providing you with actionable insights to support your research.

The timeline for results will depend on the complexity and scale of the project. As our clients often work under tight timelines, we are adept at expediting processes in the most efficient manner possible. Our team of experts will work with you to establish a timeline that meets your needs and ensures timely delivery of results.

Our team of experts uses state-of-the-art algorithms and computational methods to deliver high-quality, reliable results. During our upfront consultation, our goal is to find the most appropriate pipeline match for your research goals and project configuration. We perform quality control checks and validation throughout the bioinformatics analysis process to ensure that our results are accurate and trustworthy. We are available for support and consultation prior to, during, and after a project to answer any technical questions.

Our standard deliverable consists of a comprehensive project report that outlines our methodology, workflow, tables, and figures. We can also tailor our deliverables to your preferences, such as intermediate files, customizing figures and tables.