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Table 4 k -mers counting results for Caenorhabditis elegans (16.4 GB FASTQ file or 2 gzipped FASTQ files of total size 4.6 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
BFCounter 4/ 0 10,407 Failed Failed Failed
Jellyfish 21/ 0 88 22/ 0 89
DSK 5/13 493 5/13 458 5/16 647 5/16 481
DSK gz 5/13 587 5/13 564 5/16 761 5/16 592
KMC 32/10 105 32/18 115 32/27 185 32/31 191
KMC 16/11 93 16/18 93 16/27 163 16/32 160
KMC gz 32/10 134 32/18 138 32/27 199 32/31 203
KMC gz 16/11 119 16/18 121 16/27 195 16/32 182
  6-core PC
DSK 5/13 1,307 5/13 1,215 5/16 2,073 5/16 1,597
DSK gz 5/13 1,268 5/13 1,151 5/16 2,017 5/16 1,518
KMC 11/11 274 11/18 343 11/27 507 11/32 553
KMC gz 11/11 233 11/18 333 11/27 514 11/32 542
  Quake-compatible counters
  32-core server
BFCounter 4/ 0 10,349 4/ 0 9,527 4/ 0 8,213 4/ 0 6,689
Jellyfish 24/ 0 143 25/ 0 132
KMC 32/31 173 32/37 179 32/42 245 32/43 243
KMC 16/32 166 16/37 154 16/43 212 16/44 214
KMC gz 32/31 184 32/37 188 32/43 247 32/43 249
KMC gz 16/32 168 16/37 165 16/43 218 16/44 230
  6-core PC
KMC 11/32 562 11/37 635 11/43 750 11/44 784
KMC gz 11/32 555 11/37 627 11/43 749 11/44 772