Fig. 3

Running time of SRAssembler. SRAssembler was run for five rounds using the Os07g26940.1 protein sequence as a query for 42 million Arabidopsis genomic read pairs. The effect on running time of pre-existing preprocessed read chunks, the size of the read chunks, and the number of processors assigned to SRAssembler were each tested and are shown as the mean of three technical replicates. As the number of processors assigned to SRAssembler rises from one to 17, completion time drops dramatically. Using larger read chunks increases the time required for preprocessing but can decrease the time of chromosome walking up to some point. The speed gains from increasing numbers of processors show diminishing returns, and vanish if the number of processors exceeds the number of read chunks