Table 1 Compression features obtained for the three high coverage WGS datasets with several compression tools. Total compression ratio is the compression ratio (original size / compressed size) of the whole FASTQ file, header, sequence and quality combined
From: Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph
Method | Compression ratio | Compression | Decompression | |||||
|---|---|---|---|---|---|---|---|---|
Total | Header | Base | Quality | Time (s) | Mem. (MB) | Time (s) | Mem. (MB) | |
SRR959239 - WGS E. coli - 1.4 GB - 116x | ||||||||
gzip | 3.9 | — | — | — | 179 | 1 | 13 | 1 |
dsrc-lossy | 7.6 | — | — | — | 9 | 1942 | 13 | 1998 |
fqzcomp-lossy | 17.9 | 35.2 | 12.0 | 19.6 | 73 | 4171 | 74 | 4160 |
fastqz-lossy | 13.4 | 40.8 | 14.1 | 8.7 | 255 | 1375 | 298 | 1375 |
leon-lossy | 30.9 | 45.1 | 17.5 | 59.3 | 39 | 353 | 33 | 205 |
scalce-lossy | 9.8 | 21.4 | 8.3 | 9.2 | 62 | 2012 | 35 | 2012 |
quip | 8.4 | 29.8 | 8.5 | 5.3 | 244 | 1008 | 232 | 823 |
mince | — | — | 16.7 | — | 77# | 1812 | 19# | 242 |
orcom* | — | — | 34.3* | — | 10# | 2243 | 15# | 197 |
SRR065390 - WGS C. elegans - 17 GB - 70x | ||||||||
gzip | 3.8 | — | — | — | 2145 | 1 | 165 | |
dsrc-lossy | 7.9 | — | — | — | 67 | 5039 | 85 | 5749 |
fqzcomp-lossy | 12.8 | 54.2 | 7.6 | 15.0 | 952 | 4169 | 1048 | 4159 |
fastqz-lossy | 10.3 | 61.9 | 7.3 | 8.7 | 2749 | 1527 | 3326 | 1527 |
leon-lossy | 21.3 | 48.6 | 12.0 | 32.9 | 627 | 1832 | 471 | 419 |
scalce-lossy | 8.2 | 34.1 | 6.5 | 7.2 | 751.4 | 5309 | 182.3 | 1104 |
quip | 6.5 | 54.3 | 4.8 | 5.2 | 928 | 775 | 968 | 771 |
mince | — | — | 10.3 | — | 1907# | 21825 | 387# | 242 |
orcom* | — | — | 24.2* | — | 113# | 9408 | 184# | 1818 |
SRR345593/SRR345594 - WGS human - 733 GB - 102x | ||||||||
gzip | 3.3 | — | — | — | 104,457 | 1 | 9124 | 1 |
dsrc-lossy | 7.4 | — | — | — | 2797 | 5207 | 3598 | 5914 |
fqzcomp-lossy | 9.3 | 23.2 | 5.3 | 15.0 | 39,613 | 4169 | 48,889 | 4158 |
fastqz(a) | — | — | — | — | — | — | — | — |
leon-lossy | 15.6 | 27.5 | 9.2 | 26.8 | 40,766 | 9556 | 21262 | 5869 |
scalce(b) | — | — | — | — | — | — | — | — |
quip | 6.5 | 54.3 | 4.8 | 5.2 | 52,854 | 776 | 46594 | 775 |
mince(a) | — | — | — | — | — | — | — | — |
orcom* | — | — | 19.2* | — | 29,364# | 27505 | 10,889# | 60,555 |