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What does a sequence alignment and variant call report look like?

Our sequence alignment and variant call reports are generated by a tool called Geneious Prime. We export a select list of variables including CDS, polymorphism types, codon change, amino acid change, and protein effect. There is a wealth of…
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How to perform an NCBI nucleotide BLAST search

We often use NCBI nucleotide Blast queries to identify DNA sequences derived from Next Generation Sequencing (NGS) runs.  This brief note describes how to use the NCBI Blast algorithm and website with NGS DNA datasets. Create an NCBI Account Before…
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How to annotate a genome with Geneious

Geneious Annotations Geneious Prime includes genome annotation features and reports.  Annotation is often used to describe the structure and function of various genomic regions, such as genes, CDS's (coding sequences), exons, introns, 5'-…
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How to create Geneious variant call reports

Geneious Reports We have numerous clients who use Geneious for bioinformatics data analysis.  They use Geneious for sequence alignments of their sample datasets against reference genomes and for the interpretation of Geneious variant call…
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Microbiome reports with Kraken

We use a variety of data analysis tools such as OneCodex and Megan6 for quantifying and visualizing metagenomic sequencing datasets. Kraken2 is a popular taxonomic classification tool for metagenomic and microbiome sequencing results. The…
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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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Geneious sequence alignment & variant calls workflow

Geneious Prime is one of many bioinformatics tools that we use to post-process sequencing datasets.  Geneious includes an extensive set of functions to perform sequence alignments of sample reads against reference genomes.  And it includes…
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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…

What’s included in “basic bioinformatics”?

The Sequencing Center provides basic bioinformatics as an inclusive service with all genome sequencing projects. Here's what you can expect to receive with each type of project. Microbial Projects FASTQ Files: All microbial sequencing projects…
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What is de novo assembly?

De novo assembly is a method for constructing genomes from a large number of (short- or long-) DNA fragments, with no a priori knowledge of the correct sequence or order of those fragments. The terminology for de novo assembly is sometimes…
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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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How to find a reference genome

The goal of many sequencing projects is to identify polymorphisms and mutations in sequenced samples.  These often include SNP's, indels, chromosomal rearrangements, and various kinds of spontaneous or induced changes in nucleotide sequence. …
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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…
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How to read Geneious variant call reports

Reading Geneious Reports We often use Geneious to generate SNP/indel variant call reports.  A truncated report is available here.  (The number of SNP's/indels in a typical report can be quite large so we only show a few records in this example).   Report…

Can I use one of my sequenced samples as a reference genome?

We are often asked if clients can submit several samples at once for sequencing and then use one of the samples as a reference genome to compare against the remaining samples.  For example, clients may have a single control sample and several…

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 use Phaster for bacteriophage bioinformatics

Phaster is a bioinformatics tool for analyzing bacteriophage sequencing data sets.  It generates a variety of phage identification and annotation results that are very useful for interpreting phage sequencing data.  Currently, Phaster contains…
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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:…