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Table 2 kmer counting time, dissimilarity calculation time, and total time as well as memory usage used by Cafe and Afann to calculate the pairwise \(d_{2}^{s}, d_{2}^{*}\), and CVTree using K=12 and M=10 among a dataset of 92 white oak NGS samples of 300 Mbp

From: Afann: bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression

 Counting (min)Calculation (min)Total time (min)Memory (Mb)
Cafe-\(d_{2}^{s}\)450.24260.24710.41916
Afann-\(d_{2}^{s}\)21.931.253.1449
Cafe-\(d_{2}^{*}\)450.24224.14764.31928
Afann-\(d_{2}^{*}\)21.914.236.1304
Afann-\(d_{2}^{*}\)-fast21.90.322.211953
Cafe-CVTree450.24295.44745.61960
Afann-CVTree21.914.136.0304
Afann-CVTree-fast21.90.322.211953
Mash min21.50.121.53
Mash opt125.625.5151.120830
Skmer minNANA111.9565
Skmer optNANA656.92556
  1. Afann-\(d_{2}^{*}\)-fast and Afann-CVTree-fast stand for the fast mode of \(d_{2}^{*}\) and CVTree supported in Afann. Running time and memory usage of Mash and Skmer were also included. Mash min and Skmer min used K=12 and s=103 which require the minimum computing power. Mash opt and Skmer opt used K=31 and s=107 which have the optimal performance among Mash and Skmer using different combinations of kmer lengths and sketch sizes as shown in Additional file 1: Table S2 and Table S3