4.3.2. Quality Assessment of Sequencing Data

The sequenced paired-end reads (raw reads or raw data) were checked for quality using FastQC (fastqc\_v0.11.5) and stored in the FASTQ file format (Babraham Bioinformatics, http: //www.bioinformatics.babraham.ac.uk/projects/fastqc/). The resulting files were pre-processed with Trimmomatic v0.36 software [87] using the following parameters: SLIDINGWINDOW: 4:15; LEADING:3, TRAILING:3; ILLUMINACLIP: adapter.fa: 2:30:10; and MINLEN:36. Reads passing these filtering steps were counted as clean reads for use in subsequent analyses. Finally, basic quality statistics on the clean reads were obtained using FastQC.

All the sequencing data (accession number: CRA000731) are available in the database of Genome Sequence Archive (GSA, http://bigd.big.ac.cn/).
