What’s included in “basic bioinformatics”?

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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 receive the raw FASTQ files directly exported from our Illumina sequencers.  Researchers can use FASTQ files as the starting point for most downstream bioinformatics and data analysis.

Geneious Variant Call Report: If you have a reference genome for us to align your sample against, we can generate a variant call report through a program called Geneious Prime.  These reports will be stored in the “Genotype” directory in a  hyperlink we send to you with your data.  Projects that are unable to provide a reference genome will not include this report.


HLA Projects

FASTQ Files: HLA projects receive raw FASTQ files directly from the sequencer.

GenDx Report: We use GenDx NGSgo and NGSengine for HLA projects.  You will receive an NGSengine report for each GenDx HLA sequencing run.


Metagenomic and Microbiome Projects

FASTQ Files: All metagenomic and microbiome projects receive the raw FASTQ files directly from the sequencer.

Microbiome Report: Depending on the project, we will deliver either a Megan6 or One Codex report that shows the taxonomic classification of all organisms present in the sequenced samples.


Additional Bioinformatics Services

In addition to the included basic bioinformatics, we often provide advanced bioinformatics for clients with more complex research objectives.  This may include:

  • De novo assembly for projects with no available reference genome
    • Please note that we can only assemble to the scaffold level and generally cannot provide a fully assembled genome
  • Aligning samples to more than one reference genome (the first sequence alignment to a reference genome is included at no additional cost)
  • Annotation services
  • BLAST searches