ForenSeq Universal Analysis Software

Before founding Sqware Logics, we built the analysis software for the first next-generation sequencing system approved for generating DNA profiles for upload to the FBI’s National DNA Index System (NDIS). We began development at Illumina, rebuilt the software at Verogen, and led its development through Verogen’s acquisition by QIAGEN.

First
next-generation sequencing system approved for the FBI's National DNA Index System, in 2019
$150M
paid by QIAGEN to acquire Verogen in 2023
7 years
leading the software, from the Illumina spin-out in 2017 to 2024
  1. SampleDNA from evidence or a reference sample.
  2. Library prepA kit prepares the genetic markers to be read.
  3. SequencingThe instrument reads them.
  4. Analysis and reportThe Universal Analysis Software sets up the run and turns the data into a result. This is what we built.
The system takes a DNA sample to an answer. The software is where the forensic analyst works.

The problem

Forensic laboratories identify people from DNA, and their results have to stand up in court. Next-generation sequencing reads many more genetic markers from a sample than earlier methods, but it also produces far more data, and the analysts who use it are forensic scientists, not bioinformaticians.

The software has to take a sequencing run all the way to a result an analyst can review, report, and defend.

What we built

We started the first version at Illumina, as part of the first next-generation sequencing workflow built for forensic laboratories. At Verogen we redesigned it as a platform.

STR analysis SNP analysis Mitochondrial DNA The next kit
Shared platform Run setup Sample management Analysis Reporting
The analysis for each kit is a module that plugs into a shared platform. Modules are packaged with Docker, so a new kit could be supported without rebuilding the rest.

The software runs on a dedicated server beside the sequencer and is used from a browser in the laboratory.

Our part

  • We led the software. Anthony Rensfield was Director of Bioinformatics and Software. Christopher Edwards managed software development, then led system architecture as Associate Director.
  • We designed and built it. The architecture was ours, and we built the path from run setup to the report an analyst signs.
  • We supported it. We ourselves handled technical support for the laboratories using the system.
  • We wore many hats. Verogen was a startup, so we pitched in beyond the software, helping with IT and whatever else needed doing.

How it turned out

We delivered our releases on schedule. In 2019 the system became the first of its kind approved by the FBI, and in 2023 QIAGEN acquired Verogen. We stayed until 2024, then started Sqware Logics.

It is also why we work the way we do: we learn the problem, then build and support the system ourselves.

We did this work as employees of Illumina and Verogen. ForenSeq and MiSeq FGx are trademarks of their respective owners.

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