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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.