Illumina Sequencing

The Center supports massively parallel high throughput sequencing using our Illumina HiSeq and NextSeq instruments. These sequencers can generate billions of bases of data per run and enable a wide variety of applications including

DNA sequencing
Gene Expression, RNASeq
Small RNA
ChIP-Seq
Amplicon Sequencing

Researchers can choose either single or paired-end reads. Multiple samples can be indexed (barcoded) and be combined in order to make the most of the system's output.

Standard (High Output) HiSeq flow cells contain 8 lanes which must all be used at the same time, but each lane may be used by a different group. Each lane can each generate up to 200 million clusters using v3 reagents or up to 250 million clusters using v4 reagents. We most frequently use v3 flow cells for running single end 50bp reads and v4 reagents for 2 x 125 bp reads.
Rapid HiSeq flow cells contain 2 lanes which can either recieve the same sample or can be split between two samples. Each of these lanes can generate up to 150 million clusters. These flow cells run much more quickly than standard flow cells. We support single and paired-end reads of 50, 100 or 150 bp on rapid runs.
The NextSeq 500 runs one sample at a time over either a mid-output flow cell (up to 130 million clusters) or a high-output flow (up to 400 million clusters). These flow cells run very quickly and the cost-per-base is very low. We support single and paired-end reads of up to 150 bp on the NextSeq 500.

For help choosing the right type of sequencing for your application, see our decision tree. Even better, contact us to discuss your experiment before begining your project. We're very happy to offer joint consultations along with representatives from the informatics group. The core will keep samples and libraries for three months after we run them. If you would like to have your remaining sample/library returned, please ask the staff. After three months, extra sample/library will be discarded.

Please send all questions to illumina_submission-list@lists.fas.harvard.edu.