The UMGC provides next-generation sequencing (NGS) using platforms from both Illumina and Pacific Biosciences (PacBio). Illumina’s technology provides short reads by sequencing tens or hundreds of millions of clusters derived from single template molecules in parallel. The PacBio Sequel instrument provides long-read sequencing capabilities.
The UMGC has three HiSeq 2500s (“Watson”, “Crick” and “Franklin”) and five Illumina MiSeqs, which provide a range of capabilities in terms of output, speed, turnaround time, and read lengths. In this section, NGS instrument options are explained.
Illumina sequencers can be run in single-read (SR) or paired-end (PE) mode. In single-read runs, sequencing proceeds from only one end of the library molecules (the “forward” direction), whereas in paired-end runs, sequencing is carried out sequentially on both ends of each library molecule (“forward” and “reverse”). SR runs are described with the nomenclature “1 x read length in bp”, (e.g. “1x50 SR”). PE runs are described with the nomenclature “2 x read length in bp” (e.g. “2x50 PE”).
“Read length” refers to the number of bases of sequence generated during a sequencing run. For SR runs, this is the length of the single read, whereas in PE runs, it refers to the length of each of the two paired reads. The read length options we offer are constrained by available reagent kits from Illumina. Note, however: the read-lengths listed below are not an exhaustive list of all possibilities. If you are interested in a “flavor” of sequencing that is not shown, please contact us.
HiSeq 2500 instruments can be run in high output or rapid run mode. High output flow cells contain 8 lanes while rapid run mode flow cells have 2 lanes. High output mode generates >220 million reads per lane whereas rapid run mode yields >120 million reads per lane. The UMGC maintains one HiSeq 2500 instrument (“Franklin”) in high output mode and two HiSeq 2500 instruments (“Watson”, “Crick”) in rapid run mode. See tabs at left for more information.
The latest iteration of Pacific Biosciences (PacBio) technology is now available at the UMGC through our recently acquired PacBio Sequel. The Sequel utilizes Single Molecule Real-Time (SMRT) sequencing technology to provide a direct readout of each base during incorporation by a polymerase. This platform enables long read sequencing (up to tens of kb), as well as direct read-out of base modifications such as DNA methylation.