BALF DNA-seq of KTR with pneumonia
For metagenomic raw reads, the data quality was firstly assessed using FastQC (version 0.12.1). The adapter sequences as well as duplicated reads were removed using fastp (version 0.23.4). Paired-end reads were merged, followed by the removal of low-complexity sequences using bbmap (version 38.84.0) (Bushnell, 2014). For metatranscriptomic libraries, the treatment of the raw reads was performed as described in our previous studies (Chen et al, 2023). The reads obtained after the above processing were considered as the clean reads. All clean reads were aligned to the human genome (GCF_000001405.39_GRCh38.p13) using bowtie2 (version 2.5.2) with the "--very-sensitive" parameter to exclude human-related sequences.