Generating burrows-wheeler-transform and a suffix array of a DNA sequence with less memory
No, there is no way to decompress .bwt or .sa files, because they are not compressed. After indexing you'll get these files, which some programs (bwa) use. They should be in the same folder as your reference fasta file. What are you trying to do with these files? To get proper help here, please explain why you need these files, and show how you made the files.