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Table 2 Comparison of the peak memory consumption of GenomeTester4, Jellyfish 2.2.0, KMC 2.2 and DSK 2.0.7 while counting 32-mers with 24 threads

From: GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists

Source sequence

H. sapiens genome

H. sapiens chromosome 14 sequencing reads (GAGE library 1)

File sizes

24 files, 3.0 Gbp

2 files, 2.55 Gbp

GListMaker

64 GiB

24 GiB

JellyFish

23 GiB

9 GiB

KMC

11 GiB

11 GiB

DSK

32 GiB

2.7 GiB

  1. For KMC, the RAM-only version was used to speed up the counting
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ISSN: 2047-217X

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