The maximum file size is 4 GB.
History information can result in large SnapGene files. You can limit History to reduce SnapGene file sizes. See the following user guide articles for more information: Trim History and Set the Ancestor Limit on History Trees.
The maximum sequence length is 1 Gbp.
Note that SnapGene performance is affected by the number of features rather than sequence length. A very long unnannotated DNA sequence will not cause issues, but when there are tens of thousands of features, for example a human chromosome downloaded from NCBI, then SnapGene performance will suffer. We plan to address this limitation in future.