CRAB
Sequencing libraries were prepared with the DNA Prep (M) Tagmentation Kit (Cat. No. 20060059; Illumina Inc., USA), which includes DNA fragmentation, tagmentation, index addition, and amplification of indexed fragments. The libraries were diluted to a final concentration of 2 nM, pooled, and sequenced on the NextSeq 1000 platform (Illumina Inc., San Diego, CA, USA) using paired-end 2150 bp chemistry. DNA concentration and fragment size distribution were assessed using the Qubit 1X dsDNA HS Assay on a Qubit 4 Fluorometer (ThermoFisher Scientific, USA) and the 2100 Bioanalyzer (Agilent Technologies, USA), respectively. Raw sequencing reads and index sequences with quality scores below Q20 were trimmed using Trimmomatic v0.39, and quality control was performed with FastQC v1.0. High-quality reads were assembled de novo using Unicycler v0.5.0, and assembly metrics were evaluated with QUAST v5.2.0.