All datasets are public and can be downloaded using fasterq-dump from sra-toolkit.
To (hopefully) reproduce or run on a different .fastq file, build fqcomp28 and run ./run_benchmark.py dataset.fastq.
The script downloads and builds fqzcomp4 and fqzcomp5, and runs these tools, fqcomp28, and gzip on a specified dataset.
Two .csv with results are produced - for single and for 8 threads.
DRR296203_1:
| Tool | Compression time (s) | Decompression time (s) | Compression ratio |
|---|---|---|---|
| fqcomp28 | 15.63 | 36.73 | 4.417 |
| fqzcomp5 -5 | 35.34 | 20.48 | 4.436 |
| fqzcomp5 -3 | 13.33 | 8.49 | 4.301 |
| fqzcomp5 -1 | 11.93 | 16.5 | 4.254 |
| pigz | 137.9 | 33.05 | 2.983 |
SRR065390_1:
| Tool | Compression time (s) | Decompression time (s) | Compression ratio |
|---|---|---|---|
| fqcomp28 | 19.37 | 36.36 | 5.874 |
| fqzcomp5 -5 | 72.5 | 86.86 | 5.891 |
| fqzcomp5 -3 | 17.79 | 16.68 | 5.602 |
| fqzcomp5 -1 | 15.65 | 16.64 | 5.359 |
| pigz | 130.49 | 33.84 | 3.651 |
SRR12285250_1:
| Tool | Compression time (s) | Decompression time (s) | Compression ratio |
|---|---|---|---|
| fqcomp28 | 10.82 | 23.7 | 8.816 |
| fqzcomp5 -5 | 69.69 | 85.36 | 9.783 |
| fqzcomp5 -3 | 15.51 | 14.85 | 8.718 |
| fqzcomp5 -1 | 13.45 | 18.16 | 8.412 |
| pigz | 120.01 | 29.82 | 5.372 |
SRR25230149_1:
| Tool | Compression time (s) | Decompression time (s) | Compression ratio |
|---|---|---|---|
| fqcomp28 | 4.15 | 7.76 | 9.644 |
| fqzcomp5 -5 | 24.55 | 27.55 | 14.12 |
| fqzcomp5 -3 | 4.68 | 2.73 | 9.207 |
| fqzcomp5 -1 | 3.36 | 1.37 | 8.826 |
| pigz | 36.02 | 5.64 | 5.659 |
SRR22543904_1:
| Tool | Compression time (s) | Decompression time (s) | Compression ratio |
|---|---|---|---|
| fqcomp28 | 1.58 | 2.69 | 8.973 |
| fqzcomp5 -5 | 11.79 | 12.29 | 12.498 |
| fqzcomp5 -3 | 2.3 | 0.72 | 8.542 |
| fqzcomp5 -1 | 1.08 | 0.45 | 8.222 |
| pigz | 12.24 | 1.73 | 5.528 |
DRR296203_1:
| Tool | Compression time (s) | Decompression time (s) | Compression ratio |
|---|---|---|---|
| fqcomp28 | 39.08 | 77.16 | 4.415 |
| fqzcomp4 | 92.32 | 114.73 | 4.557 |
| fqzcomp5 -5 | 115.44 | 75.52 | 4.436 |
| fqzcomp5 -3 | 43.09 | 25.72 | 4.301 |
| fqzcomp5 -1 | 38.28 | 25.96 | 4.254 |
| gzip | 733.44 | 41.26 | 2.987 |
SRR065390_1:
| Tool | Compression time (s) | Decompression time (s) | Compression ratio |
|---|---|---|---|
| fqcomp28 | 55.37 | 92.88 | 5.847 |
| fqzcomp4 | 97.93 | 118.1 | 6.249 |
| fqzcomp5 -5 | 226.05 | 243.94 | 5.891 |
| fqzcomp5 -3 | 57.94 | 27.45 | 5.602 |
| fqzcomp5 -1 | 44.5 | 21.85 | 5.359 |
| gzip | 716.7 | 43.49 | 3.657 |
SRR12285250_1:
| Tool | Compression time (s) | Decompression time (s) | Compression ratio |
|---|---|---|---|
| fqcomp28 | 39.6 | 74.8 | 8.813 |
| fqzcomp4 | 76.08 | 93.85 | 9.796 |
| fqzcomp5 -5 | 194.56 | 227.56 | 9.783 |
| fqzcomp5 -3 | 41.11 | 21.12 | 8.718 |
| fqzcomp5 -1 | 35.24 | 18.64 | 8.412 |
| gzip | 648.44 | 45.18 | 5.378 |
SRR25230149_1:
| Tool | Compression time (s) | Decompression time (s) | Compression ratio |
|---|---|---|---|
| fqcomp28 | 15.68 | 23.15 | 9.643 |
| fqzcomp4 | 22.91 | 28.97 | 12.815 |
| fqzcomp5 -5 | 61.65 | 68.7 | 14.12 |
| fqzcomp5 -3 | 13.57 | 5.32 | 9.207 |
| fqzcomp5 -1 | 9.05 | 4.07 | 8.826 |
| gzip | 203.55 | 11.79 | 5.667 |
SRR22543904_1:
| Tool | Compression time (s) | Decompression time (s) | Compression ratio |
|---|---|---|---|
| fqcomp28 | 4.37 | 7.64 | 8.973 |
| fqzcomp4 | 7.55 | 9.63 | 10.635 |
| fqzcomp5 -5 | 25.19 | 24.15 | 12.498 |
| fqzcomp5 -3 | 5.73 | 1.56 | 8.542 |
| fqzcomp5 -1 | 2.8 | 1.25 | 8.222 |
| gzip | 68.77 | 3.65 | 5.536 |