The SARS-CoV-2 Sequence Data from Germany contains compressed FASTA files of SARS-CoV-2 genome sequences and corresponding metadata in TSV format. The data includes detailed information for each sequence, such as a unique sequence ID, sample collection date, submitting and originating laboratories, the German federal state where the sample was collected, sequencing platform, PANGO lineage assignment, and results from both bioinformatic and metadata quality control. Some entries may also include additional contextual data like Ct values and variant designations.