Franklin’s Germline Workflow

Whole Genome

Franklin for WGS solution is an end-to-end suite of tools that help you sharpen single and family case analysis by combining AI technology with the richest genetic data available for simple SNPs and complex variants such as CNVs, ROHs, mitochondrial, and even short tandem repeats.

Used by top laboratories worldwide

SNP, CNV
and mosaic
variant calling

Automated AMP and ACMG variant classification

Collaboration with teammates and other organizations

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Franklin has been optimized for all Whole Genome Sequencing (WGS) workflows, supporting each bioinformatic step from raw data to reporting. The platform uses powerful tools for variant calling and interpretation, as well as comprehensive visualizations, to efficiently process the vast amount of sequencing data from all regions of the genome into clinically actionable results.

Streamline your genome case analysis from FASTQ to Report
using Franklin features such as:

Automated case creation

Franklin allows for efficient integration with LIMS, EMR, and your own organization’s information system through an API, and also provides various ways to seamlessly import your data in bulk. You can easily upload batches of all raw data file formats from the BaseSpace App, as well as Amazon servers, other cloud-based sources, or your local computer directly through the platform’s UI. Create not only single cases but also duos, trios, and any family pedigree using Franklin’s user-friendly interface.

Variant detection

Franklin has developed a dedicated and optimized variant detection pipeline for WGS workflows, which is able to pick up all relevant variant types using multiple variant callers. Franklin uses its own bioinformatic pipeline to identify SNPs and small insertions/deletions, combining different tools and drawing on the most fitting algorithm for each step of the detection process. For CNV detection, Rainbow, Franklin’s own proprietary algorithm, is optimized for WGS workflows and uses machine learning to identify structural variants with high confidence levels. The CNV calling model keeps retraining with new batches of samples, getting better over time. Franklin is also able to call other complex genomic variants such as deep complex indels, mitochondrial variants, and short tandem repeats, and present them in wonderful visualizations using the Whole-Genome viewer.

Variant interpretation

Franklin’s classification and prioritization engine leverages the
power of AI to help pinpoint the relevant variants for your case,
taking into molecular effect, phenotypic information, and recent
publications. Franklin presents information from more than 100
databases with prediction tools, general and specific population
frequencies, genes and diseases, and automatically classifies
variants according to the latest ACMG guidelines. The platform
works as a one-stop shop for genetic evidence, helping users
visualize all the relevant information from available sources, as
well as Franklin Community data, all curated by our dedicated
team of genetics specialists.
Use Franklin’s powerful filtering to narrow down the WGS files
from thousands of mutations to a shortlist of clinically relevant,
potentially causal variants. This comprehensive tool allows
filtering by customized virtual panels, ACMG classification,
population frequencies, ClinVar submissions, phenotypes,
genomic region and molecular effect, inheritance model and
zygosity, and more.

Community Knowledge Base

Franklin will also help you seamlessly create your own
Knowledge Base to centralize your organization’s exclusive
panel, gene and variant repository composed of your unique
historical data. Working side by side with colleagues? Franklin promotes collaboration among team members by allowing you to leave comments, share relevant information and create SOPs that work specifically for your organization.
The Franklin Community comprises more than 20,000 genetic experts from around the globe, curating their real-world evidence into the platform. All users can benefit from frequency metrics, shared publications, and even variant classifications to bootstrap their clinical analysis and increase overall diagnostic accuracy.

Reporting

Franklin’s Report Studio helps you generate completely
customizable clinical reports without any added work. After
completing the case review, users can issue and even sign off a
report that includes all relevant variants as well as their
interpretation and clinical evidence with the click of a button.
Customize a template that fits your needs, assign different roles
to members of your team, and save lots of time and effort while
ending up with a tailor-made report structure thoroughly
designed for your organization’s specific workflow.

Whole-genome sequencing is one of the most comprehensive genomic tests available today, with vast applications ranging from research to the clinic. The recent decrease in price per sample for WGS has resulted in the steady adoption of this technique in laboratories all over the world, unifying wet lab workflows and simplifying the experimental procedures for different genetic conditions,
while achieving uniform coverage of the whole genome.

However, the enormous amount of data resulting from such a thorough test can be overwhelmingly complex and translate into time-consuming dry lab processing. With Franklin, you can easily analyze WGS single and family cases to reach faster and more accurate results, filled with clinically relevant insights.