Bio Tools at Noblis

Noblis has developed in-house tools that enable advanced bioinformatic analysis in a variety of domains. Backed by a team of subject matter experts, Noblis can leverage our tools along with open source applications to quickly solve a variety of complex problems.

  • We have experts in bioinformatics, data science, microbiology and software development who work in concert to provide holistic solutions to even the most difficult problems.
  • Noblis developed tools run on high performance computing architecture and excel at analyzing very large datasets such as next-generation sequencing reads.

Using Our Application, BioLaboro, Noblis Identified Unique Genetic Sequences of COVID-19

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Diagram showing relationship between SME's, Opn source and noblis tools and how the combine to make the noblis performmance space
BioVelocity Logo

Fast and Accurate Whole Genome Indexing

BioVelocity® is a bioinformatics tool based on an innovative algorithm and approach to genomic reference indices. Using a fast and accurate hashing algorithm, BioVelocity can quickly align reads to a set of references. BioVelocity takes advantage of a supercomputing system that is a scalable, massively multithreaded platform with a shared memory architecture optimized for large-scale data analysis and data mining—resulting in faster speeds, increased functionality, increased throughput and improved accuracy over current technologies. This supercomputing system enables us to use a brute force index, built out of all possible base pair sequences of various k-mer lengths. This index is used to map against thousands of references and allows for quick alignment of the k-mers amongst them simultaneously.

Noblis’ BioVelocity is a bioinformatics tool based on an innovative algorithm and approach to indexing genomic references. Using a fast and accurate hashing algorithm, BioVelocity can quickly align reads to a set of references and, through the use of high-performance computing platforms, produce faster results, increase functionality, increase throughput and improve accuracy in a bioinformatics workflow.

BioVelocity has a variety of functions:

  • Single nucleotide polymorphism (SNP) detection – SNPs are a type of genetic variation and each one represents a difference in a single DNA building block, called a nucleotide
  • Metagenomics analysis – the application of bioinformatics tools to study the genetic material from environmental samples without first culturing the present microorganisms
  • Conserved and signature sequence detection and compression - rapidly reduce the dataset of two bins of target sequences: (1) those that are conserved between the target organism and the reference genomes and (2) those that are unique to the target organism compared to the reference genomes

BioVelocity provides insight into the molecular mechanisms of pathogen evolution, virulence, host preference, lineage calculations and the emergence of highly pathogenic strains via advanced SNP detection algorithms. Advances in sequencing technology have increased the computational demands required for processing, identifying and analyzing large, complex datasets. When it comes to dangerous pathogens, speed is critical, and BioVelocity delivers.

Want to know more about how BioVelocity works? Click here.

Pset Logo

Rapidly Detecting Genomic Changes Effecting Diagnostics

Noblis’ PCR Signature Erosion Tool (PSET) rapidly identifies genomic changes to ensure that assays are effective against the newest genomic datasets. As sequencing costs drop and thousands of new complete genomes are added to public repositories every year, the landscape of ground truth for current bacterial and viral organisms is in constant flux. Many polymerase chain reaction (PCR) assays currently used to detect agents and foodborne pathogens were designed years ago, which means they may not be effective against newer genomic data.

Noblis’ PSET which tests the binding of the new and existing primers, probes and amplicons against the latest versions of the National Center for Biotechnology Information’s (NCBI) sequence databases to determine if they still match only to their intended targets. As NCBI's database and other public databases are updated over time, newly added genome strains can highlight where primers and probes may no longer be functional or where PCR assays may detect previously un-sequenced near neighbors. Using this information, an assay provider can detect potential false hits and be better prepared to design new primers and probes when false hits become unmanageable or drop below a quality threshold for performance.

Noblis collaborates with Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense (JPEO-CBRND) Defense Biological Product Assurance Office (DBPAO) to evaluate primer-probe sets of current pathogen assays and design new primer-probe pairs for wet lab validation and development.


Noblis’ BioLaboro is a rapid signature detection, assay design and testing application powered by:

  • BioVelocity® – Noblis’ fast and accurate genome indexing algorithm
  • PSET – Noblis’ PCR Signature Erosion Tool
  • Primer3 – Open source tool which designs PCR assays

BioLaboro is a bioinformatics application developed by Noblis that identifies signature regions in a pathogen genome, designs PCR assays targeting those signatures and then tests the PCR assays computationally to determine their sensitivity and specificity. This system is broadly applicable for biosurveillance and rapidly providing and improving diagnostic assays during a crisis.

BioLaboro can be applied to quickly respond to emerging infectious diseases. It can:

  • Identify unique genomic regions and score them as possible assay targets
  • Assess the ability of existing PCR assays to detect pathogens as they evolve over time
  • Design new assays with perfect detection accuracy to identified signatures for future testing and deployment

BioLaboro’s fully functional and user-friendly interface allows users with no programming experience to leverage high performance computing to design and test new assays from scratch. The application also allows users to easily output clear and easy to understand visualizations of the data.

BioLaboro Logo

Open Source Tools


Primer3 is a tool for picking primers for PCR reactions. It considers a range of criteria such as oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities. We use Primer3 along with our signature detection process to identify potential new primer sets.


TensorFlow is an open source software library for numerical computation using data flow graphs. It was developed for conducting machine learning and deep neural networks research. We use TensorFlow to evaluate our algorithms for the classification of multi-contributor human DNA samples.

kSNP and kChooser

kSNP v3 performs SNP identification and phylogenetic analysis without genome alignment or the requirement for reference genomes.

kChooser determines the optimum k-mer size for a dataset and calculates FCK, a measure of diversity of sequences in the dataset.


Cytoscape is an open-source software platform for visualizing molecular interaction networks and biological pathways; it integrates these networks with annotations, gene expression profiles, and other state data. We use Cytoscape for many different applications, including generating temporal graphs, associating genetic drift with antimicrobial resistance and even predicting stock market movements. It's great for visualization of discovered relationships and further analysis of relationship networks.

Serovar Identification Tool

SeqSero is a novel web-based tool for determining Salmonella serotypes using high-throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies.