SquiDBase: a community resource of raw nanopore data from microbes

Area of Science:

• Genomics
• Bioinformatics
• Microbiology

Background:

• Nucleotide sequences are shared in FASTQ/BAM formats but originate from diverse, platform-specific raw data.
• Oxford Nanopore Technologies (ONT) raw signal data hold biological insights for basecaller optimization and modification detection.
• Sharing raw nanopore data is hindered by technical issues and lack of standardized infrastructure.

Purpose of the Study:

• To establish a centralized repository for raw microbial nanopore sequencing data.
• To overcome limitations in storing and sharing valuable raw nanopore sequencing data.
• To support the development of computational tools and enhance open science practices.

Main Methods:

• Developed SquiDBase, a repository for raw microbial nanopore sequencing data with linked processed data and metadata.
• Created SquiDPipe, a Nextflow pipeline for automated removal of human reads from raw nanopore data.
• Sequenced 24 clinically relevant viruses and integrated public reference datasets and community contributions.

Main Results:

• Established SquiDBase, a dedicated, open-access platform for raw microbial nanopore sequencing data.
• Implemented automated human read removal for raw nanopore data.
• Integrated diverse datasets, including viral and reference data, into the repository.

Conclusions:

• SquiDBase facilitates raw data sharing, reproducibility, and the development of computational tools for nanopore sequencing.
• The platform supports open science principles within the microbial genomics community.
• Addresses critical infrastructure gaps for raw nanopore data management and utilization.