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HLA publication list for GenDx

We vet our vendors carefully before using products in our sequencing workflows.  The Sequencing Center uses the GenDx libraries for NGS (Next Generation Sequencing)-based HLA typing.  The combination of substantial immunological research,…
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How to read HLA reports

We deliver detailed HLA reports to clients immediately after their HLA sequencing runs are complete. The reports include information about HLA allele typing calls, allele ambiguities, and relevant metadata. HLA Loci The full set of HLA loci…
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Trimming Illumina adapter sequences

Adapter Sequences During the library preparation process, Illumina adapter sequences are annealed to sequencing reads.  The adapter sequences are required for attaching reads to flow cells and for attaching indexes to reads.  When sequencing…
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What are unmapped reads?

Save Unmapped Reads One of the most common activities we perform is the sequence alignment of sequenced bacterial samples against known reference genomes.  The alignment process generates two types of output: mapped reads and unmapped reads.…
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HLA nomenclature

The standardized HLA gene and allele nomenclature is managed by the WHO Nomenclature Committee for Factors of the HLA System.  A high-level summary of their nomenclature system is reproduced here for easy reference.  A thorough and detailed…

How to access your sequencing data

When sequencing runs are finished, we automatically upload FastQ files to a client's Box.com account. These files are typically found in the directory: ClientName-> Reports-> ReportID-> FastQ The FastQ files in this directory…
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How to read FastQ files

FastQ File Format Illumina sequencing instruments generate FastQ files when a sequencing run is finished.  FastQ files are the starting point for all downstream bioinformatics data analysis.   The file name suffix for a FastQ file is:…