Deduplication of files or other data or objects in a manner that is aware of a format of the file and the application. A file may be chunked based on the format. The chunks are more consistent and lead to higher deduplication ratios. The file may be presented as a single file. However, the file is stored in chunks or subfiles and deduplication is performed with respect to the chunks. When the file is read, the file is rebuilt from its respective chunks. The files may also be compressed using differential compression, which leverages the content of similar files to compress a current file.