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Both the HiSeq and the Genome Analyzer support de novo sequencing with extended read lengths, high passed-filter read counts, and the option to run lanes as paired-end for additional read length and long-range sequence information.
Sample Submission Guidelines
Users may submit unprepared genomic libraries to the BioMicro Center for Sample Prep followed by Illumina sequencing, or they may submit already-prepared libraries directly to sequencing.
Standard Illumina protocols for sample preparation can be found here. Illumina Paired End sample preparation kits can be purchased directly from Illumina or through the BioMicro Center for $3,600.00 plus shipping costs (10 sample preps per kit). To request an order or for more information please contact Kevin Thai. Ready-for-sequencing samples should be gel-purified according to your protocol and contain least 5uL of solution at a concentration of at least 10 nM in EB/ Tween 0.1%. Quality control will be run on all submitted samples.
Samples generated using standard kits with Illumina PCR primers can be submitted without sequencing primers. Sample preparations using customized PCR primer sequences should be submitted with a complementary sequencing primer.
Images acquired from the solexa sequencer are processed through the bundled solexa inage extraction pipeline to get the sequence and quality score for each base. The data is aligned to a reference genome, if requested, using an interative ELAND algorithm. An in-depth QC report is included in the package.