The MiSeq is a benchtop sequencer with workflows optimized for speed and ease of use. It uses a single flowcell single lane format and houses an on-board analysis suite, MiSeq Reporter. The Genomic Services Lab will sequence samples at any requested read length, however read lengths greater than 250 bases are not currently supported by Illumina and are not recommended by the Genomic Services Lab. MiSeq runs will be made available in BaseSpace and shared with the user upon run start. Typically, fastq files and/or any analysis files generated from MiSeq sequencing runs are available for download through BaseSpace. Data can also be made available through the Genomic Services Lab website upon request.
MiSeq flowcells are only available in a paired-end format, resulting in the inability to sequence libraries prepared with adapters specific for sequencing on a single-end flowcell. Slight differences exist in the sequences of the primers grafted onto the flowcell surfaces between the two flowcell types. Libraries prepared with single-end specific adapters must be sequenced on a HiSeq 2000 or HiSeq 2500. A vast majority of libraries are now prepared with paired-end adapters and thus are compatible with MiSeq flowcells, even if sequencing in a single-read format. If you are unsure of whether or not your library was prepared with single-end or paired-end adapters, please contact the manufacturer of the kit used to create your libraries. The Genomic Services Lab may also be able to assist you in determining the format of your adapters, if you are able to provide adapter sequences.
The single lane format of MiSeq flowcells does not provide for the opportunity to choose a control lane when sequencing low diversity libraries. To compensate for the lack of diversity, PhiX must be added to the library prior to sequencing at higher concentrations (20%-50%) than required for sequencing on a HiSeq 2000. The addition of PhiX assists in generation of the template, phasing/prephasing values, and the crosstalk matrix. In general, the lower the diversity of the library, the higher the percentage of PhiX required to produce high quality sequence. Any type of library with an inline barcode will also require PhiX spike-ins regardless of the diversity of the library. Examples of library types that display a lack of diversity include Amplicons, Methyl-seq libraries such as RRBS, and 4C, 5C, and HiC. ChIP-seq and miRNA-seq libraries can also display a lack of diversity depending on the experimental design. Upon sample submission, please make sure to provide the Genomic Services Lab with any information regarding the diversity of your library.
The HiSeq X Ten System is the most powerful sequencing platform ever created. The system consists of a set of 10 HiSeq X ultra-high-throughput instruments that are capable of delivering over 18,000 human genomes per year. The HiSeq X Ten makes human whole-genome sequencing more affordable and accessible than ever before.
The Illumina HiSeq X Ten System is designed specifically for whole-genome sequencing of human-derived samples and can only run in 150 PE mode.
The HiSeq 2500 extends the capabilities of the HiSeq 2000 and can be run in High Output Mode or Rapid Run Mode. In High Output Mode, it functions identical to a HiSeq 2000, using the same flowcells/reagents and producing the same quantity and quality of data. Rapid Run Mode utilizes the rapid sequencing chemistry initially developed for the MiSeq, including on-board cluster generation. The HiSeq 2500 in Rapid Run mode utilizes a new two lane flowcell design, in which a single sample is bifurcated over two lanes during on-board clustering. The Genomic Services Lab will sequence samples at any requested read length, however read lengths greater than 150 bases are not supported by Illumina. There are no restrictions on sample submission for Rapid Run sequencing, as a single sample is sequenced per flowcell. Although the standard format is to sequence a single sample per Rapid Run flowcell, there is also the option to sequence a different sample on each of the two Rapid Run flowcell lanes. Using a cBot, two seperate samples are hybridized to separate lanes of a Rapid Run flowcell, followed by the initial extension. The flowcell is then moved to the HiSeq 2500, where the remainder of cluster generation is carried out prior to sequencing. There are additional costs associsated with splitting two samples over a Rapid Run flowcell, due to the use of extra kits/reagents.
The single sample format of Rapid Run sequencing on the HiSeq 2500 creates similar problems to the MiSeq when sequencing low diversity libraries. High concentration PhiX spike-ins must be used for sequencing low diversity libraries in Rapid Run Mode. There also is the option of using one of the two lanes as a PhiX control lane to assist in phasing/prephasing calculation and Matrix generation.