Table 5. Run time profile of the ISMU pipeline with three datasets (WGRS, RAD and RNAseq).

Datasets	WGRS	RAD	RNAseq
Method (aligner-SNPcaller)	BWA-samtools	Bowtie-samtools	SOAP2-CbCC
Total number of cores	18	18	18
Total number of genotypes	4	10	2
Input file size (Gigabytes)	105	19.4	6.2
Total time (hours)	26.25	4.5	2
Disk space (Gigabytes)	250	57	17.5
Peak memory (Gigabytes)	45	48	3.6

Three datasets (WGRS, RAD and RNAseq) were analysed independently with 18 processors on a 48 GB RAM Linux based machine. The disk-space used for analysis, peak memory used and the total time for the run were recorded. Analysis of RNAseq dataset was quicker than RAD/WGRS datasets owing to both small input size and smaller reference sequence pseudo-molecules/contigs. The disk space requirements were found to be proportionate to data size.