Fig. 3

Throughput and percentage of correctly mapped reads for Bowtie2 when the mapping parameters were varied (gray circles and boxes). The black triangle shows the performance for the Bowtie2 default settings. While BWA-MEM and NextGenMap results using their default settings are shown as a blue triangle and a yellow triangle, respectively. Symbols above the dotted horizontal line show an increase in mapping accuracy if compared to Bowtie2 default, whereas symbols right of the dotted vertical line represent parameter settings with increased throughput. The ‘A’ arrow points to the parameter combination that achieved the highest accuracy, whereas the ‘S’ arrow marks the parameter combination with the highest throughput. The numbers in parenthesis behind the input data (D1, D2, D3) are the total runtimes needed to evaluate all parameter combinations on the respective data