Sequencing technologies at UGC
We provide both long and short read technologies at UGC, each system with it's specific properties.
After sequencing, we provide at least a basic level of bioinformatic analysis. Read more about what we offer in bioinformatic support.
Data is delivered to Uppmax by GRUS, in collaboration with SNIC.
PacBio Sequel utilizes the Single Molecule Real Time Sequencing technology which provides high sensitivity, high throughput and fast turnaround times. With longest reads spanning up to 70 Kb, it is suitable for all types of de novo genome sequencing and analysis of structural variation. Other typical applications include metabarcode studies and pooled amplicons, as sequencing bias toward shorter fragments is low. Since no amplification is required prior to sequencing, methylations in genomic DNA can be detected by analyzing interpulse duration times.
For more information about the Sequel system, visit PacBio's official site
Ion Torrent S5
The Ion S5TM XL is a high throughput sequencer that combines and upgrades characteristics of Ion PGM and Ion Proton (now discontinued at UGC). It produces read lengths up to 600 bp. Typical applications include AmpliSeq Transcriptome workflow for human and mouse genomes, as well as for other types of clinical research with a variety of gene and disease panels.
For more information regarding the Ion S5 system, visit Thermo Fisher Scientific's official site
After sequencing, we perform a quality control to make sure that the delivered data meet our standards. A basic bioinformatic analysis, including de novo assembly of small genomes (<100 Mb) and reads of insert consensus analysis, is also included in the sequencing service.
Secondary analyses can be offered for a fee, depending on the aim of the project.
For delivery of data we collaborate with SNIC-UPPMAX, Uppsala University's resource of high-performance computers, and sequencing data from NGI will be delivered to a project at the delivery resource "GRUS" hosted by SNIC-UPPMAX.
When a sequencing project is ready for delivery, NGI registers a new delivery project with the Swedish National Infrastructure for Computing (SNIC) and data is moved to GRUS. The principal investigator (PI) of the sequencing project will be assigned as the PI of the delivery project. Initially, the PI is the only member and the only person who can access the data on GRUS. Through the SNIC User and Project Repository (SUPR) web interface, the PI can administer the delivery project and add or remove members, as well as assigning a Technical Administrator and a Proxy for the PI. Members of the delivery project are able to retrieve the data from GRUS using any of the methods described in the GRUS user guide.
Data analysis can then be performed using the UPPMAX compute clusters. For more information about SNIC-UPPMAX and how to set up a UPPNEX project for data analysis, please visit the SNIC-UPPMAX webpage
For FAQ and more information about data delivery, please visit the NGI Order Portal.