Oxford Nanopore

Nanopore sequencing, the only technology that offers:

  • Direct DNA/RNA sequencing: The only technology that sequences the native strand, without optics or amplification. Simpler workflows, direct epigenetic information.
  • REAL Real-time: Real time streaming of sequence data allows rapid insight into samples, on-demand sequencing and dynamic workflows.
  • Ultra-long reads – up to 2 Mb: Determined only by fragment length: as many as 2 million bases may be sequenced in single continuous reads.
Consultation and Assistance

Contact for Genomics and Bioinformatics Consultation

Please use this link to send an email to Dr. Magdy Alabady for consultation on new or existing Genomics and Bioinformatics projects. Also, you can contact Dr. Alabady for assistance with grant proposals and for obtaining a letter of support from GGBC.

For technical questions about existing or new Nanopore projects, please contact the following Lab Managers/Staff:
• Julia Portocarrero (jportocarrero@uga.edu) for gDNA and RNA preparation and sequencing questions.
• Kateryna Stoianova (kstoianova@uga.edu) for cDNA and amplicon preparation and sequencing questions.

For general questions, please review the rest of our website before contacting a lab member.

More contacts
Please visit our “All Inquiries” page for detailed information about who you should contact at GGBC to receive a quick and accurate response.

Sample Preparation

General Submission Guidelines

  • Please submit your order form before sending in samples.
  • If you are submitting more than 24 samples, put the samples in a 96-well plate and include and Excel file with the sample layout in your order form.
  • Clearly mark all sample submissions with your order number.
  • Include any QC information (Qubit data, Bioanalyzer or Fragment Analyzer run, gel picture, etc) about your sample on your order form.
  • DNA should have absorbance ratio values of 1.8 – 2.0, and be submitted in 1x TE.
  • RNA samples should be suspended in RNase-free water, or 1x TE buffer prepared with RNAse-free water.

Preparation-Specific Guidelines
Libraries prepared at the GGBC can be sequenced on the Flongle or MinION Nanopore flow cells. If you have a project for Oxford Nanopore Sequencing and do not see a library preparation for your experiment, please contact us for custom sequencing.

Preparation-Specific Guidelines

 Flongle (FLO-FLG106)MinION (FLO-MIN106)
Yield per flow cell1-2 Gb15-30Gb for DNA
1-3 Gb for RNA
Channels per flow cell126512
Price per flow cell$122*$999*
Run time1 min - 16 hours1 min - 48 hours

*see pricing tab for more information on costs

 

We offer library preparation for gDNA, amplicons, cDNA, and direct RNA. Not all library preparation types are compatible with both flow cells. See the chart below for details about each type.

Library Prep
Method
DNA Ligation Direct RNARapid LigationAmplicon/
cDNA Ligation
16 S
Coming soon:
Amplicon/cDNA with barcoding
Input
requirements
500ng-1ug of dsDNA500ng-1ug RNA400ng HMW gDNA100-200 fmol amplicons or cDNA10ng gDNA0.5nM amplicons/cDNA
Shearingoptional Covaris shearingnoneyesnonenonenone
Mulitplexednonononoyes, up to 12 samplesyes, up to 96 samples
Nanopore
Catalog #
SQK-LSK109SQK-RNA002SQK-RAD004SQK-LSK109SQK-RAB204EXP-PBC096
Flongle/MinION compatibilitycompatible with bothnot for Flongle currentlycompatible with bothnot for Flongle currentlynot for Flongle currentlynot for Flongle currently

 

DNA Ligation

The DNA Ligation library preparation is best for double-stranded DNA, with optional fragmentation. This protocol does not use PCR. This library prep will include a positive control strand to help distinguish between sample failure and library prep failure in troubleshooting. The control strand is a 3.6kb amplicon from the Enterobacteria phage Lambda genome. If you are using this protocol for long reads, please make sure to submit high-molecular weight DNA.

  • Please submit 500ng-1ug of double-stranded DNA

Direct RNA

The Direct RNA library preparation is for sequencing direct RNA sequencing. This protocol does not use PCR. Input RNA should have a 3’ polyA tail. On the MinION, this will yield 1-3 Gb, when starting with high-quality RNA.

  • Please submit 500ng-1ug of RNA

Rapid Ligation

The Rapid Ligation preparation is a shorter protocol for sequencing gDNA. The protocol does not use PCR, and uses transposase-based fragmentation. The read length will have a random distribution, depending on the input fragment size.

  • Please submit 400ng of high-molecular weight gDNA

Amplicon/cDNA Ligation

The Amplicon/cDNA library preparation is for sequencing shorter DNA fragments, such as amplicons and cDNA. This protocol does not use PCR. Currently, this preparation is only for single-samples, not multiplexing. Submit cDNA samples pre-made. For amplicons, you can either submit gDNA and your region-specific primer sequences and we will make the amplicons, or you can submit your amplicons directly. We will only make amplicons when the target size is <1,000 bp.

For pre-made amplicons and cDNA:

  • Please submit 1-1.5ug of long double-stranded DNA, or 100-200 fmol for short fragments

For gDNA, to be made into amplicons by GGBC:

  • Please submit 500ng-2ug of gDNA
  • Please submit your primer sequences

16S sequencing

The 16S library preparation is for sequencing the entire 16s rRNA region. This protocol uses PCR. Amplicons can be barcoded for up to 12 samples.

  • Please submit 10ng of gDNA

 

Coming soon: Amplicon/cDNA with barcoding for 1-96 samples

The Amplicon/cDNA  library preparation with barcoding is for sequencing multiple samples on the same flow cell. This protocol does use PCR, and can barcode up to 96 samples.

Prices and Quotes

Table 1. Oxford Nanopore single sample library preparation fees

Library TypeUGA FeeNon-UGA FeeCommercial Fee
Direct RNA single sample library prep$416$491$624
PCR free cDNA seq single sample library prep$263$311$395
cDNA seq single sample library prep. PCR included.Coming soonComing soonComing soon
DNA single sample library prep with rapid ligation$204$241$306
DNA single sample library prep with ligation$253$299$380
Amplicon single sample library prep with ligation starting from amplicon $263$311$395
Amplicon single sample library prep with ligation starting from gDNA $548
$647
$822

Table 2. Oxford Nanopore multiplexed samples library preparation fees

Library TypeUGA FeeNon-UGA FeeCommercial Fee
Multiplexed DNA library prep with ligation (per sample)$95$113$143
Multiplexed DNA library prep with ligation (per pool)$142$168$213

Table 3. Oxford Nanopore multiplexed amplicons library preparation fees

Library TypeUGA FeeNon-UGA FeeCommercial Fee
Multiplexed 2-48 amplicons library prep starting from gDNA$1,047$1,236$1,571
Multiplexed 49-96 amplicons library prep starting from gDNA$1,663$1,963$2,495
Multiplexed 2-48 amplicons library prep starting from amplicon DNA$642$758$963
Multiplexed 49-96 amplicons library prep starting from amplicon DNA$1,032$1,218$1,548

Table 4. Oxford Nanopore sequencing run pricing

Run TypeUGA FeeNon-UGA FeeCommercial Fee
Flongle flow cell$122$144$183
1D flow cell$999$1,179$1,499

Data Retrieval
      1. Data files will be transferred to customers through the GGBC’s data distribution FEX server. This will include the fast5 and fastq files from reads that passed and failed quality checks, duty time and throughput reports, and Nanopore run summary files.
      2. The data files will be permanently deleted from GGBC’s data storage after 6 months from the data transfer date.