Table 2.

Data sets used for testing findNeighbour performance

Dataset	Sites called	Links less than SNP stored	Memory usage	Mean time to add one sample
A: M. tuberculosis, n = 15,985 mapped to NC_000962	329,714 sites excluded	20	23.5G	2.23 s
B: Neisseria gonorrhoea, n = 2455 mapped to NC_011035	All sites included	500	19.3G	2.95 s
C: Salmonella enterica, n = 5380 mapped to AM933172	51,897 sites excluded	20	7.4G	1.77 s

Data sets studied and FindNeighbour2 performance

The data sets studied, which can be downloaded at https://ora.ox.ac.uk/objects/uuid:82ce6500-fa71-496a-8ba5-ba822b6cbb50 are described. Also shown are performance characteristics of Findneighbour2 operating on them using the hardware in Additional file 2