UWBC Illumina Sequencing Policies
Please thoroughly review these policies prior to submitting samples. If you have any questions regarding
this policy or any other aspect of next generation sequencing, please contact us at nextgenseq@biotech.wisc.edu.
Sample Submission:
Projects will not be entered into the Illumina run queue until samples and completed submission form
are in the possession of the DNA Sequencing Facility. Once samples are entered into the queue, UWBC
will give you a tentative run date. We strive to honor this run date; however, there are issues beyond our
control that may delay your run. Further, a flowcell will not be run until all lanes are filled. In the event
of a delay greater than a week, UWBC will email users to inform them of an updated run date. In order
to expedite sequencing, samples may be placed on any run that meets or exceeds the requested
parameters. Typical turnaround time is 6 weeks.
User Responsibilities:
 Dropped off samples must be prepared to UWBC specifications. Submission guidelines can be
found on the DNA Sequencing webpage
(http://www.biotech.wisc.edu/services/dnaseq/sequencing/Illumina)
 The organism name and sequence of a phylogenetically analogous reference genome (e.g. hg19
for Homo sapiens) must be supplied, if available.
UWBC Deliverables (per lane/chip):
 MiSeq (minimum): 12M reads passing filter, 70% bases Q30 (99.9% accuracy) or greater
 HiSeq2000/2500 (minimum): 125M reads passing filter, 80% bases Q30 (99.9% accuracy) or
greater
 Amplicon libraries (minimum): 20,000 reads per submitted sample.
 A FASTQC and Run Summary Report will be delivered for each library. These files provide
overviews of run quality. Reads will not be trimmed for any reason.
 Data are delivered in FASTQ format within 5 business days of run completion. Further analysis
may be contracted separately with the Bioinformatics Resource Center (BRC) at
brc@biotech.wisc.edu.
 Libraries that do not meet these specifications will be re-run at the earliest possible date;
however, there may be a wait for a run that will meet or exceed the requested parameters.
Exceptions:
While we will make every effort to create successful sequencing runs with high quality data output, we
cannot be responsible for improperly prepared samples. Therefore, we make no guarantees on the
quantity and quality of data generated from Illumina sequencing if:
1. Libraries are prepared by the user, as we have minimal control over quality.
2. Samples are submitted that do not meet UWBC minimum submission requirements.
3. Non-Illumina barcode/index methods are used. Barcodes placed at the 5’end of the sequence
and those with no redundancy are especially prone to read errors.
4. Species are sequenced for which there is no reference genome available.
If your data do not meet these criteria, or if you have other questions/concerns regarding your data,
please contact us immediately at nextgen-seq@biotech.wisc.edu to address your concerns.
Minimum and Optimal Sample Requirements:
If the following initial QC requirements are not met you will be informed via email. You may elect to
either resubmit samples of sufficient quality and quantity or proceed with the existing samples. Should
you choose to proceed with samples that do not meet our requirements, the samples will be run AS IS,
and we make no assurances on the quality of downstream data.
Options for resubmission:
 If concentrations are too low:
o Additional sample material can be submitted. No substitutions will be accepted; only
additions can be made to the original submission. Additional QC of this material will be
done at the lab’s expense ($1.50/sample).
o The entire sample submission can be returned to the submitting lab. The lab is
encouraged to precipitate or purify the DNA and elute in an appropriate volume. Vacuum
centrifugation is discouraged as it will also concentrate inhibitors.
 If concentrations are too high:
o The entire sample submission can be returned to the submitting lab and the sample(s) in
question can be diluted appropriately from the measurements provided by the UWBC.
o The staff at the UWBC can perform sample dilution ($1.50/sample).
Data Storage:
Deliverable sequence data will be stored in your download directory. These files will not be removed by
the DNA Sequencing Facility. We store the raw, .bcl file output from each sequencing run for 60 days.
If you wish to have a copy of this data, you must contact the DNA Sequencing Facility prior to the
beginning of your sequencing run.