This repository provides information-reproducibility on how compressible a human genome sequence is (T2T Chm13 version 2.0 [article,sequence]) using different data compressors.
The 3,117,292,120 human DNA symbols have been compressed (lossless) to
| Rank | Bytes | Bps | Time (m) | RAM (GB) | Program | Replication | Factor (*) |
|---|---|---|---|---|---|---|---|
| 1 | 538,155,679 | 1.381 | ? | ? | JARVIS3 | ? | |
| 2 | 539,129,963 | 1.384 | 641 | 13.7 | JARVIS3 | ||
| 3 | 543,855,534 | 1.395 | 381 | 28.8 | JARVIS2 | ||
| 4 | 544,059,173 | 1.396 | 389 | 28.8 | JARVIS2 | ||
| 5 | 544,267,353 | 1.396 | 420 | 27.4 | JARVIS2 | ||
| 6 | 544,292,577 | 1.397 | 399 | 26.9 | JARVIS2 | ||
| 7 | 545,960,947 | 1.401 | 283 | 26.9 | JARVIS2 | ||
| 8 | 549,594,830 | 1.410 | 284 | 11 | JARVIS2 | ||
| 9 | 550,041,600 | 1.411 | 340 | 18.8 | JARVIS2 | ||
| 10 | 550,051,840 | 1.411 | 309 | 18.8 | JARVIS2 | ||
| 11 | 550,379,520 | 1.412 | 279 | 18.7 | JARVIS2 | ||
| 12 | 554,823,680 | 1.423 | 253 | 18.7 | JARVIS2 | ||
| 13 | 554,985,480 | 1.424 | 219 | 4.1 | JARVIS2 | ||
| 14 | 555,412,871 | 1.425 | 690 | 24.8 | GeCo3 | ||
| 15 | 555,679,745 | 1.426 | 616 | 24.3 | GeCo3 | ||
| 16 | 555,977,522 | 1.427 | 488 | 22.2 | GeCo3 | ||
| 17 | 556,415,717 | 1.428 | 427 | 19.7 | GeCo3 | ||
| 18 | 557,100,364 | 1.430 | 428 | 17.2 | GeCo3 | ||
| 19 | 557,438,004 | 1.431 | 426 | 15.7 | GeCo3 | ||
| 20 | 557,995,100 | 1.432 | 406 | 14.6 | GeCo3 | ||
| 21 | 558,343,430 | 1.433 | 396 | 13.3 | GeCo3 | ||
| 22 | 559,124,034 | 1.435 | 425 | 11.6 | GeCo3 | ||
| 23 | 560,694,405 | 1.439 | 354 | 12.8 | GeCo3 | ||
| 24 | 560,982,904 | 1.440 | 416 | 8.1 | GeCo3 | ||
| 25 | 561,644,781 | 1.441 | 280 | 11.3 | GeCo3 | ||
| 26 | 562,253,393 | 1.443 | 281 | 11.3 | GeCo3 | ||
| 27 | 564,282,192 | 1.448 | 222 | 6.3 | GeCo3 | ||
| 28 | 564,613,120 | 1.449 | 82 | 4.5 | JARVIS2 | ||
| 29 | 564,913,725 | 1.450 | 262 | 7.3 | GeCo3 | ||
| 30 | 566,108,106 | 1.453 | 54 | 8.4 | JARVIS2 | ||
| 31 | 566,387,531 | 1.454 | 215 | 6.3 | GeCo3 | ||
| 32 | 575,830,095 | 1.478 | 94 | 2.9 | GeCo3 | ||
| 33 | 576,296,690 | 1.479 | 37 | 5.9 | JARVIS2 | ||
| 34 | 577,672,973 | 1.482 | 88 | 1.9 | GeCo3 | ||
| 35 | 578,588,274 | 1.485 | 101 | 3.3 | GeCo3 | ||
| 36 | 581,917,199 | 1.493 | 97 | 1.8 | GeCo3 | ||
| 37 | 583,746,074 | 1.498 | 86 | 3.3 | GeCo3 | ||
| 38 | 589,813,339 | 1.514 | 17,465 | 0.6 | nncp | ||
| 39 | 603,726,643 | 1.549 | 71 | 3.3 | GeCo3 | ||
| 40 | 607,749,667 | 1.560 | 22 | 2.5 | MFCompress | ||
| 41 | 607,835,665 | 1.560 | 48 | 1.8 | GeCo2 | ||
| 42 | 609,579,746 | 1.564 | 171 | 13.8 | JARVIS | ||
| 43 | 612,331,601 | 1.571 | 4,588 | 1.6 | paq8l | ||
| 44 | 614,339,951 | 1.577 | 39 | 28.5 | bsc-m03 | ||
| 45 | 614,919,247 | 1.578 | 39 | 20.4 | bsc-m03 | ||
| 46 | 618,241,906 | 1.587 | 39 | 16.3 | bsc-m03 | ||
| 47 | 619,369,574 | 1.590 | 20 | 2.0 | GeCo2 | ||
| 48 | 619,837,647 | 1.591 | 12 | 0.6 | MFCompress | ||
| 49 | 620,837,061 | 1.593 | 39 | 11.2 | bsc-m03 | ||
| 50 | 625,647,034 | 1.606 | 38 | 5.6 | bsc-m03 | ||
| 51 | 625,753,521 | 1.606 | 11 | 0.6 | MFCompress | ||
| 52 | 628,342,060 | 1.613 | 18 | 0.5 | GeCo2 | ||
| 53 | 639,222,915 | 1.640 | 43 | 0.8 | NAF-22 | ||
| 54 | 646,062,792 | 1.658 | 84 | 0.6 | lzma -9 | ||
| 55 | 661,591,088 | 1.698 | 36 | 0.05 | bsc-m03 | ||
| 56 | 752,793,986 | 1.932 | 5 | 0.001 | bzip2 -9 | ||
| Baseline | 779,323,017 | 2.000 | - | - | 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)/(3117292120*2)*100). The Run1.sh and Run4.sh ran in a Laptop computer running Linux with 11th Gen Intel® Core™ i5-1135G7 @ 2.40GHz × 8, 8 GB of RAM, and an SSD disk of 512 GB. The remaining computations 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 |
| JARVIS3 | code | - |
| Zstandard | code | base |
Change directory and give permitions:
cd scripts/ chmod +x Run*.sh
To replicate each run, use the respective replication script.