Do you offer genome sequencing discounts?

Yes! There are a couple of ways you save even more on your research budget. Pre-pay Discount Any project that is paid in full upfront will receive a 3% discount on the total project price. Referral Discount If you refer a colleague to our…

How to read Pillar gene panel reports

We use the PiVAT variant reporting tool from Pillar Biosciences to analyze genotyping results for several gene panels.  PiVAT generates a set of report files that are stored in the "Genotype" directory in your Box.com account. Pillar Gene…
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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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What does an HLA report look like?

Our HLA reports are generated automatically by the GenDX NGSengine® software and includes information about HLA allele typing calls, allele ambiguities and relevant metadata. The exact set of loci displayed in an HLA report will depend on…
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How to generate a complete genome with hybrid assembly

Introduction In this article, we'll describe the Unicycler hybrid assembly pipeline.  Unicycler is designed primarily for de novo assembly of bacterial genomes and includes the major steps required for hybrid assembly of sequenced microbial…
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How to perform de novo assembly with PATRIC

De novo assembly is a method for generating contigs, scaffolds, or complete genomes from Next Generation sequencing reads (i.e. DNA fragments).  Some researchers use the free, online bioinformatics tool PATRIC for de novo assembly.  PATRIC…
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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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HLA PIRCHE matching service

NGSengine can now export HLA typing results of an individual sample directly to the PIRCHE matching services website. This will facilitate laboratories to predict indirectly recognizable HLA epitopes for either hematopoietic stem cells or solid…
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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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Where to find a genetic counselor

We offer HLA (human leukocyte antigen) sequencing services for immune system and histocompatibility research.  As part of this service we deliver HLA reports that include allele typing for up to 12 HLA genes.  Genetic counselors are available…
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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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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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Protocol documents and manuals

Geneious Geneious Manual Library Prep Nextera XT Library Prep Reference Guide Miniseq Denature Dilute Libraries Guide Metagenomics - Microbiome 16S Metagenomic Library Prep Guide Quality Control BBDuk (HTML only) …

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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Microbiome reports with Megan6

We use MEGAN6 to generate microbiome reports along with a host of other analytical and visualization tools.  Here is an example of a microbiome report from MEGAN6. Fig. 1 Fig. 1 shows a phylogram of a human nasopharyngeal sample displayed…
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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…

Sequence alignments with Geneious

Geneious Alignments We often use Geneious for the alignment of sequenced samples to reference genomes. When sequencing runs are finished, our sequencers generate raw FastQ files, which typically contain millions of short DNA fragments ("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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What are HLA ambiguous alleles?

In our CareDx TruSight Assign HLA reports, ambiguous alleles are identified with a double dash (- -). For example, "- -:01:01" indicates an ambiguity in the first field, "01:- -:01" indicates an ambiguity in the second field, and "01:01:-…