This dataset, specifically generated for SquiDBase, includes sequencing data for Monkeypox virus and various RNA viruses, processed by the Clinical Virology and Virology Units at the Institute of Tropical Medicine Antwerp (ITM). Sequencing and data analysis was performed at the Adrem Data lab. The data provides a comprehensive resource for viral genomics and bioinformatics analysis.

Summary of methods

Monkeypox Virus: DNA was extracted and amplified using Sequence-Independent Single-Primer Amplification (SISPA), following the protocol by De Baetselier et al., 2022.

RNA Viruses: The protocol included RNA extraction, TurboDNase treatment, reverse transcription to cDNA, and subsequent amplification with SISPA, based on methods described by Greninger et al., 2015 and Kafetzopoulou et al., 2018.

Sequencing Details

Platform: Oxford Nanopore Technologies (ONT) MinION

Flow Cells: R10.4.1 (FLO-MIN114)

Library Preparation: Rapid Barcoding Kit v14 (SQK-RBK114.24)

Batch Size: 24 pooled samples per library

Runtime: 42–72 hours per flow cell

Output: 1.88–5.22 gigabases per flow cell

Basecalling and Data Processing

Data were processed using SquiDPipe v1.0.0 (https://github.com/Cuypers-Wim/squidpipe)