New Web Tool Validates Illumina Sample Sheets Before Demultiplexing to Prevent Errors

A research team has developed an open-source web application designed to validate Illumina sequencing sample sheets prior to the demultiplexing stage, according to a software study published in BMC Bioinformatics. Created by Laure Lemée, Rania Ouazahrou, Etienne Kornobis, and Thomas Cokelaer, the application, titled Check My Sample Sheet, provides automated sanity checks to identify configuration errors before data processing begins. The authors released the browser-based platform to address operational challenges in sequencing workflows, where incorrect metadata can compromise downstream analytical pipelines and experimental outcomes.

In high-throughput sequencing operations using Illumina platforms, proper configuration of each run is essential to achieve successful outcomes.

Because downstream analysis relies directly on the fidelity of the sample sheet, validating these files beforehand is critical for preventing avoidable errors during sequencing processes.

To make verification accessible across different laboratory environments, the developers built Check My Sample Sheet as an interactive, browser-based web application using the Streamlit framework. The platform requires no local software installation, allowing researchers and facility technicians to interact with the system entirely through a standard web browser. Users can either upload existing sample sheet files directly from local storage or paste raw text contents into a simple user interface to initiate automated analysis.

The core computational engine of the application incorporates the IEM Python module from the Sequana Python library to conduct comprehensive sanity checks on submitted files. Once a user uploads or pastes a sample sheet, the tool executes automated validation algorithms designed to examine multiple essential parameters. Specifically, the automated checks assess adherence to Illumina formatting standards, detect potential sample duplication, and evaluate the internal consistency of the supplied metadata across all recorded samples.

The application fully supports the legacy bcl2fastq format, referred to as version 1, as well as the newer bclconvert format, known as version 2 or BCL Convert. Importantly, the platform automatically detects which format version has been submitted, eliminating the need for users to manually configure format specifications before running validation checks.

By enabling investigators to preemptively detect and resolve potential issues in their sample sheets, the application helps laboratory teams reduce sequencing errors and improve overall sequencing outcomes. In addition, the authors highlighted that the open-source nature of Check My Sample Sheet supports future extensibility.

Subject of Research: Validation of Illumina sequencing sample sheets using a browser-based web application

Article Title: Check my sample sheet: a web application for validating illumina sample sheets before demultiplexing

Article References: Lemée, L., Ouazahrou, R., Kornobis, E., & Cokelaer, T. (2026). Check my sample sheet: a web application for validating illumina sample sheets before demultiplexing. BMC Bioinformatics. https://doi.org/10.1186/s12859-026-06695-7

Image Credits: AI Generated

DOI: 10.1186/s12859-026-06695-7

Keywords: Illumina sequencing, sample sheet validation, demultiplexing, Streamlit application, Sequana library, IEM module, bcl2fastq, bclconvert, BCL Convert, BMC Bioinformatics, bioinformatics software, sequencing quality control, sample metadata, open-source bioinformatics, metadata consistency, sanity checks