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Table 3 k -mers counting results for Homo sapiens HG02057 individual (208 GB FASTQ file or 6 gzipped FASTQ files of total size 65.9 GB)

From: Disk-based k-mer counting on a PC

  k=22 k=28 k=40 k=55
Algorithm Space Time Space Time Space Time Space Time
  Classic counters
  32-core server
Jellyfish 27/ 0 1,375 75/ 0 1,433
Jellyfish1 27/ 0 1,375 21/ 53 2,404
DSK 6/168 8,683 6/156 9,073 6/195 13,172 6/197 9,409
DSK gz 6/168 10,125 6/156 10,579 6/195 14,569 6/197 10,987
KMC 32/130 1,221 32/220 1,706 32/341 2,486 32/391 2,722
KMC 16/134 1,376 16/234 1,872 16/343 2,664 16/405 2,967
KMC gz 32/130 1,249 32/219 1,505 32/342 2,304 32/391 2,597
KMC gz 16/134 1,195 16/234 1,732 16/343 2,479 16/403 2,909
  6-core PC
DSK 6/168 22,963 6/156 23,512 6/195 37,958 6/197 28,681
DSK gz 6/168 21,688 6/156 22,061 6/195 36,328 6/197 26,584
KMC 11/137 2,939 11/234 3,782 11/343 6,133 11/405 7,770
KMC gz 11/136 2,623 11/235 4,041 11/343 6,306 11/405 7,020
  Quake-compatible counters
  32-core server
Jellyfish 51/ 0 2,426 59/126 2,503
KMC 32/388 2,612 32/468 3,011 32/537 3,541 32/542 3,546
KMC 16/402 2,990 16/468 3,405 16/539 4,300 16/552 4,175
KMC gz 32/387 2,409 32/468 2,860 32/537 3,370 32/536 3,357
KMC gz 16/400 2,760 16/468 3,285 16/498 4,083 16/552 4,038
  6-core PC
KMC 11/404 6,625 11/469 7,741 11/539 9,673 11/552 11,135
KMC gz 11/403 6,783 11/468 8,034 11/539 9,764 11/553 9,775
  1. Test methodology and column description are just as for Table 2. The asterisk sign (for Jellyfish) denotes that two separate databases were constructed by Jellyfish due to the memory limit of the machine (128GB RAM) and Jellyfish reported that to merge these databases it needs more RAM, so these times are underestimated.