Frequently Asked Questions
FAQ – General
Diving into sequencing for a new project and placing a sequencing order can be overwhelming. We collected some of the most commonly asked questions here (in addition to the tips and recommendations on our individual service pages) to help ease some of that pressure.
To help you navigate, the “expand all” button will open all answers to allow in-browser search functionality. If you have a question not covered here, please do not hesitate to contact us at info@seqcenter.com!
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To ensure data delivery before winter break, samples should be received at SeqCenter by Monday, December 9th. Data for orders received after that day may be delivered into the new year.
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We will be closed and unable to receive shipments starting Thursday, December 24, 2026 through Sunday, January 3, 2027. Our two-week turnaround window will also be offset for this closure. Please see our policy page for additional details.
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Tuesday, December 15th is the last day that SeqCenter recommends shipping overnight packages. Delays on all speeds of delivery are expected, and at least 1 additional day is common.
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Customers must notify us in advance of any billing deadlines they have in order for invoices to be submitted on time.
Yes, we often reattempt failed preps (for example rerunning with adjusted PCR cycles) and will discuss re‑submission options and any additional charges if the initial prep fails.
Yes, with platform‑specific requirements: Illumina libraries with adapters generally must be pooled and run on a dedicated flowcell, Nanopore libraries can be accepted but should stop before final adapter ligation so we can finish ligation and loading, and PacBio will accept fully prepared SMRTbell libraries that meet the stated volume and concentration requirements.
SeqCenter is happy to help identify which existing services may best apply to your samples. If you have a custom project, please contact our team and will help to evaluate if an existing service is applicable or if a custom preparation or analysis can be completed. Availability of custom work is subject to change and may be billed as an hourly custom service. These details will be indicating in a final custom quote before sample or data processing is started.
We will attempt to work with low‑input or out‑of‑spec samples when possible (for example concentrating extra volume, skipping redundant DNase steps, or using extra PCR cycles), but success is not guaranteed and special handling or alternative preps may be required.
Globus Compute is data a large-scale, interconnectable data transfer service that supports free-to-use accounts that can be tied to an email address or ORCID. Data can be downloaded with a free account. For more details, please visit our Globus at SeqCenter help page.
SeqCenter hosts the data for a limited timeframe and recommends downloading or transferring the data as soon as possible. (Please see our policies page for more details about our data retention timelines.) Some institutions may have existing Globus endpoints to which the hosted data can be easily transferred.
You may need permits or specific documentation depending on sample type and origin; follow Category B/CDC guidance and any country‑specific export/import rules and discuss regulated or restricted strains with us before shipping. Please contact us if you are unsure.
SeqCenter is a BSL2+, RUO laboratory and is happy to accept samples within those specifications. Projects requiring clinical certifications such as CAP/CLIA unfortunately cannot be accepted. Organisms classifeid as BSL3 or greater cannot be accepted. Please contact SeqCenter directly if you are unsure if we can accept your samples.
We accept international shipments provided they comply with shipping regulations and any required permits; follow the appropriate Category B/CDC and carrier rules and notify us in advance so we can advise on paperwork and handling.
We offer DNA, RNA, and dedicated flowcell short read sequencing on our Illumina machines, as well as long read sequencing on Oxford Nanopore and PacBio machines. For additional information, please visit our pipeline overview and specific service pages using the “Services” navigation menu.
We unfortunately do not offer Sanger sequencing services.
Yes, SeqCenter offers a variety of standard bioinformatic services or more customer services depending on your needs. Please evaluate our standard offerings listed here or contact us with you specific request.
We provide results and analysis deliverables via Globus in a project folder and typically include FASTQ, BAM, VCF, HTML reports, CSV metrics, PDFs, and assemblies; raw Nanopore POD5 files are retained for no less than 90 days.
Data is uploaded to our Globus endpoint and then shared with the customer in two ways. An invite is sent out via Globus to the primary email address of the order, giving the customer access and permission to share and transfer the data. An additional link to the data is sent by email to the same address as a shortcut, and will only work for Globus accounts that have already accepted the original invite. We highly recommend that customers download local copies of all data or transfer to their own endpoint for storage beyond our hosting timeline. Please see our policies page for more information on our data retention window.
We are able to accommodate alternative distribution methods, though these may be delivered outside of the two-week window and may require additional setup. Please contact us if you would prefer an alternative method.
We commonly use tools such as FastP for QC, alignment tools (BWA, STAR), taxonomic profilers (MetaPhlAn, Kraken) for metagenomes, Cell Ranger for 10x data, variant callers (Breseq for haploid, GATK for diploid), and downstream packages for differential expression (edgeR, DESeq2) depending on your experiment.
Choose a provider that offers the platforms and library preps you need, performs the QC and handling your samples require (HMW, low input, regulated shipping), provides the deliverables and file formats you expect, and can support any custom analysis or turnaround constraints you have.
Quote generation (and order processing) for our standard services is handled directly through our website. To obtain a quote, you only need to complete through Step 2, after which an email with a pdf quote is sent to the address entered. You are more than welcome to create as many quotes as you would like, and there is no obligation to cancel a quote. To return to a quote at a later date, you can either use the hyperlink provided in the quote email or the “Access a Quote” tab from our homepage.
For service requests outside of our standard packages, please contact us for a custom quote.
To generate a valid sequencing quote, you will need to know basic inforamtion about the material you wish to submit for sequencing. If submitting extracted material, please have the sample names and their concentrations ready before placing an order. If an extraction will be ordered during quote generation, please know what sample type will be submitted as well as what media/buffers you plan to use when shipping your samples. Please note that for international customers, we do not recommend shipping live cells as they will likey be halted in customs and may be returned.
We recommend keeping samples cold or frozen (ship on dry ice when required), using stabilizers like RNAlater or DNA/RNA Shield for room‑temperature transport when appropriate, avoid repeated freeze–thaw cycles, send extra volume for low‑concentration samples so we can concentrate them on arrival, and note special handling instructions on the sample sheet so our team can QC and process samples promptly.
You can proceed straight from quote generation to order submission directly through our website. If you already generated a quote, you can return to an existing quote by using either the hyperlink in the quote email or the “Access a Quote” tab from our homepage.
To complete checkout, you are required to complete Step 3 (Sample Details) and Step 4 (Submit Payment). In Step 3, you are prompted to input sample names, concentrations, and select which samples are receiving analysis, if applicable. In Step 4, payment information (credit card or purchase order) is added.
Only custom quotes/orders need to be placed with a SeqCenter representative.
Quotes are typically valid for 90-days. Please note that some custom quotes may have expiration dates that deviate from this standard validity window.
All of our standard services are guaranteed within a two-week turnaround window, which is set by the date upon which we receive all pieces of an order. This includes all samples, a payment method, and any additional files or information needed to process the order and analyses. Specific data outputs are unique to each of our services and can be found in the individual service’s page using the “Services” drop down arrow from our home page.
We unfortunately cannot guarantee results sooner than two weeks, though we make our best efforts to deliver all orders as quickly as possible.
Custom projects and quotes are not covered by the two-week guarantee, but every effort is made to stay as close to the two-week window as possible.
We only ask that the methods section states that the specific services ordered were performed by SeqCenter in Pittsburgh, PA, with service specifics being derived from the methods documents provided with each order.
Before the samples arrive at our facility, we recommend keeping a close eye on the courier tracking for your shipment in case of any unexpected shipping delays. Once the package arrives at our facility, our team carefully reviews the samples and corresponding order.
After an order is reviewed, you will receive an automated email from us notifying you that your samples arrived. If the team has any questions or comments, these are listed in the email. There may be a small delay between when the courier marks a package as delivered and when you receive your notification, and occasionally these notifications are flagged as spam. Please check your spam if you do not see an email.
Our facilities will be closed for specific holidays, and we will be unable to accept packages during those days. Additionally, the closures will offset the two-week deadline for orders for which the turnaround window includes the dates listed below. (Please see our policies page for more information on our two-week turnaround window.)
2026 Closures
- Monday, Jan 19, 2026 (Martin Luther King Jr. Day)
- Monday, Feb 16, 2026 (US Presidents’ Day, Washington’s Birthday)
- Monday, May 25, 2026 (US Memorial Day)
- Monday, Sept 7, 2026 (US Labor Day)
- Monday, Oct 12, 2026 (Indigenous People’s Day/Columbus Day)
- Thursday, Nov 26, 2026 through Sunday, Nov 29, 2026 (US Thanksgiving)
- Thursday, Dec 24, 2026 through Sunday, Jan 3, 2027 (Winter Break)
We are happy to help get you started with your analysis, though we cannot provide interpretations or support for third party programs. If your order included analysis, the analysis methods document includes additional information and resources which can provide a great launching point, as well.
If you are looking for a bioinformatic program with a graphical interface, Galaxy and Geneious are two popular and powerful tools, with plenty of documentation. KBase is also a fantastic cloud-based platform that hosts many common command-line packages in point-and-click format along with a large plethora of premade pipelines and tutorials.
Additionally, we offer several standard add-on analysis packages and would love to discuss what custom analysis services we are able to provide for your specific project, if the standard services do not meet your needs.
Of course, if there are any issues with your data, please contact us so that we can begin investigating immediately.
Please send us an email or contact our team through the contact us form on our website. Rush handling fees may apply and availability will be dependent on current queues and instrument run times.
Unfortunately, at this time, most adjustments to existing quotes and orders are not possible through our website.
If you would like to add samples or analyses to your quote order, please place a new, separate order for the additional services (or a replacement order).
If the changes only apply to sample names and sample concentrations, we are able to make the corresponding changes internally. Please reply to either your order confirmation email or the email that shared the quote with details of the changes.
If you would like to decrease the number of samples on your order, please make note of the decrease during your submission. We will remove the samples that are no longer required from the order during the billing process. You are only billed for the samples that were sequenced.
For any analysis requiring a reference, provide any one of the following:
- Assembly file (ending in ONLY .gb, .gbff, .gbk, .tar, .fasta, .fa, .fna).
- Annotated files (.gb, .gbk, .gbff) files are required for RNA analysis and recommended for variant calling, as the output will include gene information.
- .fna and often .fasta files contain nucleotide information only.
- NCBI Accession Number as text in the Comments box. (Accession numbers start with GCA, GCF, NC, etc.)
- Please ensure that the number provided aligns to the annotation set you want.
- GenBank and RefSeq annotations will differ in locus tag and can differ in number of predicted orfs or functional annotations. The customer must choose one or the other.
- Nanopore Combo or Assembly sample from current or previous order, including the order number, referenced as text in the Comments box.
Common issues include low template concentration, primer‑dimer or short‑insert artifacts that survive cleanup, and inhibitors carried over from extraction; note that handling and extraction method strongly influence amplicon success.
The most common causes we see are low input concentration, contaminants that inhibit tagmentation or bead binding (phenol, iron/metal contaminants, EDTA), and severely degraded or nicked DNA that fragments unpredictably during prep; when preps fail we often reattempt with maximum recommended PCR cycles and extra QC.
Long‑read failures are usually due to poor high‑molecular‑weight DNA quality (nicks or shearing), contaminants that interfere with ligation or polymerase activity, and insufficient input mass for HMW protocols; for some samples (e.g., modified phage genomes) base modifications can also prevent successful library construction or sequencing.
We deliver common outputs including FASTQ (.fastq.gz), BAM (.bam), VCF (.vcf), JSON (.json), CSV (.csv), HTML (.html), PDF (.pdf) and assembled sequences (FASTA); pipeline outputs (for example DRAGEN) include these file types.
The exact output varies by service. Please see the individual service pages for full file lists.
In general, all sequencing orders will include at least raw reads in fastq format, a methods document, and a summary of some overall sequencing statistics for each sample. The .fastq files are raw, unassembled reads with adapter sequences trimmed.
We need organism and estimated genome/transcriptome size, primary goal (assembly, variant calling, RNA‑seq, microbiome), desired coverage or reads per sample, number of samples, read structure (single/paired and read length), indexing scheme, expected fragment size or HMW status, sample concentration/volume, and any custom probes or references so we can size flowcells, estimate yield, and advise library prep and QC.
Coverage (breadth) describes how much of the target region or genome is represented by at least one read (often reported as a percentage), while read depth (sequencing depth) is the average number of times a given base is sequenced (expressed as “×”, e.g., 30×); depth affects confidence in base calls and rare‑variant detection, whereas breadth/coverage indicates how much of the target is actually observed.
Short‑read sequencing produces high‑accuracy, relatively short fragments ideal for variant calling and expression quantification, while long‑read sequencing yields much longer contiguous reads that resolve repeats and structural variants and improve de novo assemblies, though long reads have different error profiles and input DNA requirements.
Unfortunately, we do not offer expedited service. Our guaranteed turnaround time of two weeks is an industry best and is representative of many other sequencing service providers’ expedited service times.
We are happy to try to accommodate high priority orders as we can, free of charge, but we cannot guarantee that we will meet a specific deadline that falls before the end of the standard two-week window.
Minimums depend on platform and workflow: some methods can be viable down to ~0.2 ng/µL but we do not recommend below ~5 ng/µL for standard preps; PacBio HMW workflows typically require ~2 µg total HMW DNA, and prepared SMRTbell libraries should be 50 µL at ≥20 ng/µL
We recommend >50 ng/µL in 20–40 µL (≈1 µg total) for standard rRNA‑depletion RNA‑seq, we have seen success down to ~10 ng/µL in some cases with extra volume or special handling, and for Nanopore direct RNA we expect ~300 ng polyA RNA or ~1 µg total RNA for a single flowcell.
Confirm concentrations and volumes, note low‑concentration samples on the sample sheet and send extra volume if possible, follow shipping rules for regulated material and frozen shipments (dry ice) where required, and include clear sample‑sheet notes so our staff can perform appropriate QC and handling on arrival.
We recommend using Illumina Connected Multiomics for the analysis of Illumina Protein Prep (IPP) data. Don’t have access to this software? SeqCenter’s bioinformaticians can help!
The turnaround time for all orderable services through the website is 2 weeks or less. This means that you will receive access to the sequencing data within 2 weeks of SeqCenter receiving your samples. Please note that the turnaround time is contingent on an order being completed through our website and SeqCenter having received all items needed to fully process your order. Please also note that the 2 week turnaround time does not apply to custom work.
We are able to accept a wide variety of sample types for DNA/RNA extraction, including frozen cell pellets, growth on agar plates, agar slants. We also accept other common environmental sample types including water samples, soil, stool, and swabs. SeqCenter cannot extract sufficient amounts of DNA from a single colony.
Please note that this is not an exhaustive list of the samples that SeqCenter can accept. If you are unsure if we accept your sample type, please contact us in advance of shipping samples.
Coverage (breadth) describes how much of the target region or genome is represented by at least one read (often reported as a percentage), while read depth (sequencing depth) is the average number of times a given base is sequenced (expressed as “×”, e.g., 30×); depth affects confidence in base calls and rare‑variant detection, whereas breadth/coverage indicates how much of the target is actually observed.
The window starts once we receive all necessary parts of the order, including all samples, a payment method, and any information needed to process the samples or analyses. If any additional information is needed or an order is modified, the timeframe will be reset.
Unfortunately, custom services and orders are not covered in this two-week turnaround time. We will still target this two-week window, but the timeframe for custom work cannot be guaranteed.
Our library preparation pipelines are very robust and accommodate a wide range of sample qualities. As such, we will attempt library preparation for all samples submitted as they are.
We ask our customers to evaluate the quality and quantity of their samples before sending and ensure they meet our submission standards as well as requirements of their project. In some instances, we are able to accommodate samples submitted below requirements, but custom arrangements must be made in advance. Please refer to each specific pipeline’s service page for recommendations for submissions, our submission FAQ page for information about samples that do not meet our requirements, and our policies page for more information on our failed sample policies.
