Software | Implementation | Website | Lossless / | Ambig. | Var. | Speed of | Ratio | Random | Methods | Remarks |
---|---|---|---|---|---|---|---|---|---|---|
name | availability | lossy | codes | length | compr./ | access | ||||
src code / binaries / libs | reads | decompr. | ||||||||
Compressors of raw sequencing data | ||||||||||
gzip | C++ / many / many | yes / no | yes | yes | moderate / very high | low | no | LZ, Huf | ||
bzip2 | C / many / many | yes / no | yes | yes | low / high | low | no | BWT, Huf | ||
7zip | C, C++ / many / many | yes / no | yes | yes | low / very high | moderate | no | LZ, AC | ||
BWT-SAP [21] | C++ / — / C++ | yes / no | yes | no | low / low | moderate | no | BWT, PPM | FASTA only | |
DSRC [17] | C++ / Lin, Win / C++, Pyt | yes / no | yes | yes | high / high | moderate | yes | LZ, Huf | ||
Fqzcomp [30] | C / Lin / — | yes / yes | no | yes | high / moderate | high | no | CM | ||
G-SQZ [31] | C++ / Lin / — | yes / no | no | no | high / moderate | low | yes | Huf | ||
Kung-FQ [19] | C# / Win / – | yes / yes | no | no | moderate / moderate | moderate | no | AC, LZ, RLE | ||
Quip [29] | C / – / – | yes / no | no | no | high / high | high | no | M. models, AC | ||
ReCoil [20] | C++ / — / C++ | yes / no | no | no | very low / high | moderate | no | BWT, PPM | FASTA only | |
SCALCE+gzip [22] | C++ / – / – | yes / yes | no | no | moderate / high | moderate | no | AC, LZ, Huf | ||
Seq-DB [28] | C++ / – / – | yes / yes | no | no | very high / very high | low | yes | AC, LZ, RLE | ||
SeqSqueeze1 [30] | C/ Lin/ — | yes / no | no | yes | very low / ver low | high | no | CM | ||
Compressors of reference genome alignment data | ||||||||||
gzip | C++ / many / many | yes / no | yes | N/A | low / very high | low | no | LZ, Huf | ||
bzip2 | C / many / many | yes / no | yes | N/A | low / high | low | no | BWT, Huf | ||
7z | C, C++ / many / many | yes / no | yes | N/A | low / very high | moderate | no | LZ, AC | ||
BAM [32] | C++ / many / many | yes / no | yes | N/A | moderate / high | moderate | yes | LZ, Huf | ||
CRAM [33] | Java / many / Java | yes / yes | yes | N/A | moderate / moderate | moderate | yes | Huf, Gol, diff. | ||
Quip [29] | C / – / – | yes / no | no | N/A | high / high | high | no | M. models, AC | ||
SAMZIP+rar [34] | C/ – / – | http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028251 | yes / no | yes | N/A | moderate / high | moderate | no | RLE, LZ, Huf | |
Compressors of single genome sequences | ||||||||||
gzip | C++ / many / many | yes / no | yes | N/A | moderate / very high | low | no | LZ, Huf | ||
bzip2 | C / many / many | yes / no | yes | N/A | low / high | low | no | BWT, Huf | ||
7z | C, C++ / many / many | yes / no | yes | N/A | low / very high | moderate | no | LZ, AC | ||
dna3 [35] | C / – / – | yes / no | no | N/A | low / low | moderate | no | LZ, PPM | ||
FCM-M [36] | C / – / – | yes / no | no | N/A | very low / very low | moderate | no | M. models | ||
XM [37] | Java / many / Java | yes / no | yes | N/A | very low / very low | moderate | no | M. models, AC | ||
Compressors of genome collections | ||||||||||
gzip | C++ / many / many | yes / no | yes | N/A | low / very high | very low | no | LZ, Huf | ||
bzip2 | C / many / many | yes / no | yes | N/A | low / high | very low | no | BWT, Huf | ||
7z | C, C++ / many / many | yes / no | yes | N/A | low / very high | high | no | LZ, AC | chr-ordered | |
ABRC [38] | C++ / Lin, Win / C++ | http://www2.informatik.hu-berlin.de/~wandelt/blockcompression/ | yes / no | yes | N/A | high / very high | very high | yes | LZ, Huf | |
GDC [39] | C++ / Lin, Win / C++ | yes / no | yes | N/A | high / very high | very high | yes | LZ, Huf | ||
GReEn [40] | C / – / – | yes / no | yes | N/A | high / high | high | no | M. models, AC | ||
GRS [41] | C / Lin / – | yes / no | yes | N/A | moderate / low | high | no | LCS, Huf | ||
RLZ [42] | C++ / – / – | yes / no | yes | N/A | moderate / very high | high | no | LZ, Gol |