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Pacific Biosciences Sequencing

Cold Spring Harbor Laboratory is an HHMI designated Pacific Biosciences (PacBio) sequencing site. We provide PacBio sequencing services to all HHMI investigators located at nearby non-profit research institutions.

We currently have an HHMI beta project grant in place that will fund sequencing projects, using a maximum of 16 SMRT cells. This beta program is designed to encourage HHMI investigators to make use of this technology.  Priority is given to HHMI investigators, but services are also offered to CSHL investigators.

Eric Antoniou
This e-mail address is being protected from spambots. You need JavaScript enabled to view it
(516) 422-4003

Sequencing Service:
PacBio_seqWe offer full service sequencing on the Pacific Biosciences RS instrument. We will QC the DNA, make the PacBio sequencing library and sequence the library on the appropriate number of SMRT cells.

Furthermore, we will help you design your sequencing experiment (insert size, type of run, number of SMRT cells, etc.) to help ensure that you will receive the data you need for your research.

Final Data:
Because PacBio sequencing libraries are made from circular DNA molecules with hairpin loops (adapters) ligated at both ends of the DNA insert, the raw sequence reads often contain multiple instances of the DNA insert sequence, separated by the adapter sequences. We remove the adapter sequences, breaking up the raw reads into sub reads. Each sub read contains the partial or entire DNA insert sequence (depending on the read length of the raw sequence). The subread sequences are provided in a fastq formatted file on our FTP server.


PacBio technology revealed:

Current performance of the Pacific Biosciences RS sequencer:
 A typical SMRT Cell will generate between 40,000 and 50,000 reads. After filtering (using a 10 kbp insert library), the maximum read length is 25-26 Kbp. The average read length is around 3500bp with the P4 enzyme and around 8500bp with the new P5 enzyme.

The error rates are as advertised by the company, about 12% (P4 enzyme) -16% (P5 enzyme) with a single pass over a template.   Hence, in the long read mode, your DNA molecule would be sequenced a single time with this overall error rate. In the circular consensus mode (CCS), a molecule would be sequenced several times, and the consensus sequence (CCS) error rate will be considerably lower (exact error rate depends on the number of individual sequences used to generate the CCS sequence).

Details of the full range of applications can be found at the PacBio applications page;

For understanding accuracy in SMRT sequencing, see the following document;

Costs for HHMI investigator ONLY. Other external customers must contact the core manager, Eric Antoniou ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ), for pricing.  DNA Sequencing Shared Resource

Per sample QC



Sequencing Library Prep








SMRT cell sequencing