Subject	Biological sciences
Specific subject area	Omics: Transcriptomics Virology
Type of data	Raw BAM files Figure Table
How the data were acquired	Sequencing – Oxford Nanopore MinION R9.4 SpotOn and Flongle Flow Cells Basecalling – Guppy 3.6 Statistics – in house script (https://github.com/moldovannorbert/seqtools)
Data format	filtered data: after basecalling, reads were filtered based on quality score (Qscore ≥ 7) and passed mapped reads are stored in BAM files
Description of data collection	Various cell cultures were infected with six human pathogen RNA viruses. Total RNA was isolated from the infected cells at different time points after viral infection. Libraries were generated and then sequencing reactions were carried out on a MinION (Oxford Nanopore Technologies) device. Guppy 3.6 was used for basecalling and minimap2 for aligning the raw reads to the viral and host genomes.
Data source location	Coxsackievirus (CVB5) •Institution: Public Health and Food Chain Safety Service of Government Office for Csongrád County, Laboratory Department •City/Town/Region: Szeged •Country: Hungary West-Nile virus •City/Town/Region: Vojvodina •Country: Serbia •2013 Influenza type A virus - subtype H1N1 •Institution: National Center for Epidemiology •City/Town/Region: Budapest •Country: Hungary
	Vesicular stomatitis Indiana virus •Institution: Department of Medical Microbiology and Immunobiology, University of Szeged •City/Town/Region: Szeged •Country: Hungary Crimean–Congo hemorrhagic fever virus •City/Town/Region: Balkan Peninsula Zika virusInstitution: European Virus Archive
Data accessibility	The available BAM files containing the reads aligned to the reference genomes are available at ENA and can be used without restrictions. Repository name: European Nucleotide Archive (ENA) Data identification numbers: PRJEB46600 (H1N1), PRJEB46591 (CCHFV, WNV and ZIKV), PRJEB46598 (CVB5), PRJEB46127 (VSIV) Direct links to the dataset: https://www.ebi.ac.uk/ena/browser/view/PRJEB46600 https://www.ebi.ac.uk/ena/browser/view/PRJEB46591 https://www.ebi.ac.uk/ena/browser/view/PRJEB46598 https://www.ebi.ac.uk/ena/browser/view/PRJEB46127 Supplementary files are available at figshare: doi:10.6084/m9.figshare.19228416