RNA-seq of human: Lower respiratory tract infections
Adaptor sequences and low-quality bases were removed from raw sequencing reads by the AfterQC program (version 0.9.6). For ethical reasons, human reads were subsequently removed by mapping against the entire human reference genome (GRCh38) using the HISAT2 (version 2.2.1) program. For de novo assembly, trimmed and high-quality reads were assembled into contigs using Trinity (version 2.12.0). All human tombus-like virus related reads were extracted by mapping against the human tombus-like virus genomes obtained in this study.