SquiDBase
A resource for storing and sharing raw nanopore sequencing data from microbial and viral research projects.
Our mission: Advancing open science and addressing data challenges in nanopore sequencing.
In the rapidly evolving field of nanopore sequencing, researchers and developers face several significant challenges.
Voluminous data
Raw nanopore data, or 'squiggles', are large and complex, making them difficult to store and manage effectively.
Dataset fragmentation
Squiggle datasets are currently dispersed across multiple databases, making it challenging to compile specific subsets needed for algorithm development or benchmarking existing tools. Furthermore, certain meta-analyses depend on access to squiggle data, highlighting the need for a more centralized and accessible solution.
Resource intensity
Managing the massive volume of squiggle data requires substantial storage capacity, which can be cost-prohibitive.
Data reusability
The raw format of squiggle data often lacks structured metadata, which is crucial for enhancing their reusability and making them accessible for research and development.
Privacy concerns
Ensuring the automated removal of human genetic information from squiggle data to maintain privacy and compliance with regulations.
SquiDBase: Easy sharing of your raw nanopore sequencing data
SquiDBase is an innovative platform designed to manage and share large amounts of microbial and viral nanopore sequencing data, enhancing the capabilities of researchers and scientists in pathogen detection, genomic analysis and algorithm development. Committed to open science and reproducibility, we emphasize the importance of sharing raw nanopore data accompanied with sufficient metadata. Main Features of our platform include:
- User-Friendly Interface: Find data efficiently with our intuitive interface designed to facilitate easy data upload and download.
- POD5 support: SquiDBase accepts POD5 files, the current standard for ONT uploads, along with structured metadata.
- Accessible submissions: Gain straightforward access (no login required) to a vast number of submissions, making it easier to retrieve and utilize the data you need.
Join our global research community
We support open science and collaboration as key drivers of scientific progress. SquiDBase aims to be more than a tool; it aims to become a platform for researchers focused on advancing genomic research through shared knowledge and innovation.
Invitation to contribute
Contribute your research, share your data, and access a wealth of data that grows as our community does. By joining SquiDBase, you're not only accessing a dynamic database of microbial sequence data; you're also contributing to enhance pathogen detection and genomic studies.
Our Team
Wim L. Cuypers
Lead Researcher
Halil Ceylan
Lead Developer
Eline Turcksin
Lab Technician
Julia M. Gauglitz
Promotor
Wout Bittremieux
Promotor
Kris Laukens
Promotor
Nicky de Vrij
Contributor
Tessa de Block
Contributor
Koen Vercauteren
Contributor
Kevin K. Ariën
Contributor
Philippe Selhorst
Contributor
Contact us
We'd love to talk about how we can help you.
Ask Your Questions
Have questions about SquiDBase or how you can use it in your research? Don't hesitate to ask! We're here to help guide and provide the information you need.
Fill Out Our Survey
We have a couple of questions related to our squiDBase resources, which will be aimed at collecting and sharing Raw Nanopore data (or so called 'squiggles').
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