This repository provides information-reproducibility on how compressible a cassava genome sequence is (TME 204 [article,sequence]) using different data compressors.
The 762,392,783 cassava DNA symbols have been compressed (lossless) to
| Rank | Bytes | Bps | Time (m) | RAM (GB) | Program | Run | Factor (*) |
|---|---|---|---|---|---|---|---|
| 1 | 69,078,516 | 0.7249 | 193,0 | 11,3 | JARVIS2 | 18 | |
| 2 | 70,063,509 | 0.7352 | 163,2 | 5,9 | JARVIS2 | 17 | |
| 3 | 71,522,417 | 0.7505 | 114,4 | 2,9 | JARVIS2 | 19 | |
| 4 | 76,069,141 | 0.7982 | 162,4 | 24,8 | GeCo3 | 7 | |
| 5 | 76,274,590 | 0.8004 | 89,9 | 19,7 | GeCo3 | 8 | |
| 6 | 76,349,440 | 0.8012 | 45,3 | 1,2 | JARVIS2 | 21 | |
| 7 | 76,361,940 | 0.8013 | 89,3 | 8,1 | GeCo3 | 10 | |
| 8 | 76,381,495 | 0.8015 | 80,6 | 11,6 | GeCo3 | 9 | |
| 9 | 77,864,398 | 0.8171 | 47,6 | 7,3 | GeCo3 | 11 | |
| 10 | 77,946,880 | 0.8179 | 28 | 4 | JARVIS2 | 22 | |
| 11 | 79,370,240 | 0.8329 | 18 | 2 | JARVIS2 | 20 | |
| 12 | 80,345,790 | 0.8431 | 33 | 4 | JARVIS2 | 16 | |
| 13 | 81,267,289 | 0.8528 | 22 | 2 | GeCo3 | 12 | |
| 14 | 81,387,520 | 0.8540 | 12 | 5 | JARVIS2 | 23 | |
| 15 | 82,134,490 | 0.8619 | 25 | 2 | GeCo3 | 13 | |
| 16 | 86,065,540 | 0.9031 | 130 | 6 | JARVIS1 | 15 | |
| 17 | 88,607,613 | 0.9298 | 9 | 2 | GeCo2 | 4 | |
| 18 | 89,470,912 | 0.9388 | 11 | 3 | GeCo2 | 5 | |
| 19 | 91,378,688 | 0.9589 | 20 | 3 | GeCo3 | 14 | |
| 20 | 93,208,245 | 0.9781 | 4 | 2 | MFC-3 | 32 | |
| 21 | 93,681,287 | 0.9830 | 13 | 1 | LZMA-9 | 25 | |
| 22 | 93,992,979 | 0.9863 | 8 | 3 | NAF-22 | 24 | |
| 23 | 96,085,325 | 1.0083 | 8 | 9 | BSC-m03 | 27 | |
| 24 | 97,255,512 | 1.0205 | 4 | 2 | GeCo2 | 3 | |
| 25 | 98,576,956 | 1.0344 | 2 | 1 | MFC-2 | 31 | |
| 26 | 99,411,034 | 1.0431 | 2 | 1 | MFC-1 | 30 | |
| 27 | 99,943,268 | 1.0487 | 8 | 5 | BSC-m03 | 28 | |
| 28 | 100,623,483 | 1.0559 | 15 | 1 | GeCo3 | 6 | |
| 29 | 104,672,000 | 1.0984 | 4 | 1 | GeCo2 | 2 | |
| 30 | 111,431,846 | 1.1693 | 2 | 1 | GeCo2 | 1 | |
| 31 | 133,792,919 | 1.4039 | 8 | 0 | BSC-m03 | 29 | |
| 32 | 169,616,349 | 1.7798 | 1 | 0 | BZIP2-9 | 26 | |
| Baseline | 190,598,196 | 2.0000 | - | - | 2 BPS | - |
(*) The base line of 2 bits per symbol is used to calculate the (data compression) Factor, which represents the proportion of the sequence that has been fully compressed and is given by 100-((CompressedBytes*8)/(762392783*2)*100). Experiments ran in a Desktop computer running Linux with Intel® Core™ i7-6700 CPU @ 3.40GHz × 8, 31,2 GiB RAM, and disk of 3 TB. The ranking is given by the lowest number of bytes (Kolmogorov complexity approximation).
| Data Compressor | Repository | Description |
|---|---|---|
| GeCo3 | code | article |
| GeCo2 | code | article |
| paq8l | code | article |
| nncp v3.1 | code | article |
| NAF | code | article |
| lzma 5.2.5 | code | article |
| JARVIS | code | article |
| bzip2 1.0.8 | code | article |
| MFCompress | code | article |
| bsc-m03 v0.2.1 | code | article |
| JARVIS2 | code | article |
Change directory and give permitions:
cd scripts/ chmod +x *.sh Install_Tools.sh GetCassava.sh RunCassava.sh