| Format | Compressor | Version | Options | Levels |
| fasta | cat | 8.22 | cat | none |
| sz | snzip | 1.0.4 | snzip -c | none |
| lz4 | lz4 | 1.6 | lz4 -c | -1 to -9 |
| gz | gzip | 1.6 | gzip -c | -1 to -9 |
| bz2 | bzip2 | 1.0.6 | bzip2 -cz | -1 to -9 |
| br | brotli | 1.0.7 | brotli -c | -q 0 to -q 11 |
| zstd | zstd | 1.3.8 | zstd -c | -1 to --ultra -22 |
| xz | xz | 5.2.2 | xz -zkc | -0 to -e9 |
| zpaq | zpaq1 | 7.15 | zpaq a | -m1 to -m4 |
| blast | blast1 | 2.6.0+ | makeblastdb -dbtype nucl -title '' | none |
| 2bit | faToTwoBit1,2 | ? | faToTwoBit -long | none |
| mfc | mfcompress1 | 1.01 | MFCompressC | -1 to -3 |
| dlim | deliminate1 | 1.3c | delim a | none |
| naf | ennaf | 1.0.0 | ennaf | -1 to -22 |
1 Operates via wrapper due to inability to pipe input or output or other deficiencies.
2 Wrapper stores ambiguous IUPAC nucleotides separately.