Whole genome sequencing of Lactococcus lactis: strain CNM81 isolated from raw milk
Genomic DNA quality and concentration were assessed using agarose gel electrophoresis, NanoPhotometer, and Qubit fluorometer. Libraries were prepared from 1 g DNA using the NEBNext DNA Library Prep Kit, involving DNA fragmentation (~350 bp), end repair, A-tailing, adapter ligation, and PCR enrichment. Library size distribution and concentration were evaluated by Agilent 2100 Bioanalyzer and qPCR. Paired-end sequencing (150 bp) was performed on the Illumina NovaSeq 6000 platform.Raw reads were quality-checked with FastQC and trimmed with Trimmomatic. Clean reads were aligned to the reference genome using Bowtie2. Variants were called and filtered with bcftools and functionally annotated using SnpEff. MultiQC was used to aggregate quality reports.