An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data

BMC Genomics

Table 1 AAF performance metrics

Coverage	Filtered	Memory (MB)	Generating k-mer table (CPU hours, using one core)	Calculating distance matrix (CPU hours, using one core)
5X	no	68,082	117	103
5X	yes	68,086	85	56
2X	no	39,780	66	61
2X	yes	39,048	39	22
1X	no	34,316	50	8

Performance metrics for the AAF reconstruction of the 11-primate phylogeny from simulated SRS data using one thread only. Phylogenetic reconstruction requires generating the k-mer table and calculating the number of shared k-mers between species to compute the distance matrix. Note that the memory usage is for the first step; the second step required no more than 1G of memory

ISSN: 1471-2164