Kocuria rhizophila SA117
Library preparation:NEBNext Ultra II DNA Library Prep Kit for IlluminaNEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs)Library QC:Agilent Bioanalyzer 2100 High sensitivity DNA KitKAPA Library Quantification Kit for IlluminaRaw data were automatically processed by Basespace cloud interface (Illumina) in default settings. The basecalling, adapter clipping, and quality filtering were carried out using bcl2fastq v2.20.0.422 Conversion Software (Illumina).De novo assembly, gene prediction and annotationThe quality of raw reads was checked using programs FastQCv0.11.8 and MultiQC v1.9. Adapter sequences and reads with lower quality than Q25 were filtered out by cutadapt (v2.6). Trimmed reads were aligned to the reference genome of Kocuria rhizophila DC2201 and contigs newly assembled using Burrows-Wheeler Aligner (BWA-MEM, 0.7.17-r1188). The quality of alignments was evaluated by Qualimap (v.2.2.2-dev). Trimmed reads were assembled de novo using SPAdes genome assembler (v3.13.1) with multi k-mer sizes (21, 33, 55, 77) and minimal contig size 300bp. The quality of the resulting de novo assembly was evaluated by Quality Assessment Tool for Genome Assemblies (QUAST v5.0.2) using the reference genomes of Kocuria rhizophila DC2201 (see in 202113275_Assembly/)