Franklin’s Germline Workflow

Low Pass Sequencing

Franklin for LPS solution is an end-to-end suite of tools that help you sharpen pre- and post-natal case analysis by combining AI technology with the richest genetic data available for all complex copy number variants and rearrangements, such as deletions, duplications, mosaics and trisomies.

Used by top laboratories worldwide

Validated detection
of CNVs and
rearrangements

Automated AMP and ACMG variant classification

Collaboration with teammates and other organizations

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Franklin has developed our own validated Low-Pass Sequencing (LPS) workflow, supporting each bioinformatic step from raw data to reporting. The platform uses powerful tools for precise 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 low-pass 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. In addition to the sample-specific
quality control indicators, you can also have QC metrics for
each batch, both with customized thresholds to help with
quality assurance and benchmarking of your workflow.

Variant detection

Franklin has developed a dedicated and optimized variant
detection pipeline for low-pass genome workflows, which is
demonstrated to pick up all the variants detected by microarray.
For CNV, mosaic and trisomy detection, Rainbow, Franklin’s
own proprietary algorithm, is optimized for low-pass workflows and uses machine learning to identify structural variants with high confidence levels . The pipeline utilizes read depth, SNP information, split reads, and reads which map to two different sites in the genome, providing overall effective genome-wide resolution of 3,000 bp. In addition, the CNV calling model keeps retraining with new batches of samples, getting better over time, which results in high sensitivity and specificity detection of structural variants.
On top of that, we are currently in the process of validating our bioinformatic pipeline to identify SNPs and small indels from LPS, offering a cost-efficient solution for the detection of all types of variants across the genome.

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, automatically-calculated ACMG classification, and recent
publications. Franklin presents information from  more than 100
databases including prediction tools, general and specific
population frequencies, genes and diseases, with dedicated
tools for complex genomic copy number variations, ClinGen
curated recommendations, and more. 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.

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.


Low-pass sequencing has recently emerged as a cost-effective alternative to genotyping arrays to identify genetic variants that influence multifactorial traits in the clinic. This high-throughput sequencing of the entire human genome at low coverage (around 5x) provides an accurate, affordable and high-capacity resource to identify variants, especially CNVs with great specificity and sensitivity. LPS is a new powerful technique that is starting to become widely applied in the context of prenatal and postnatal genetic analysis.

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 low-pass genome sequencing single and family cases to reach faster and more accurate results, filled with clinically relevant insights.

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