Performance evaluation on RRBS data.

Performances comparison on real-life libraries among GPU-BSM, Bismark, BSMAP, and BS-Seeker2. A directional library SRR748751, which consists of 11.961.710 reads of length 100 bp has been analyzed. The first and second column of the table report the library and the name of the tools, respectively. The third column reports the time required to analyze the library. Columns 4 to 9 report the percentage of uniquely mapped reads according to the number of mapping differences. Differences are mismatches when the tools are used to look for ungapped alignments, whereas they may be mismatches and/or indels when the tools are used to look for gapped alignments. Computing time for GPU-BSM has been reported running it on a single and on two GPUs. As for multi-threading based tools, computing time has been reported for 12 cores. Tools settings: i) GPU-BSM -m 5 –ungapped -l 1 -R -d C-CGG, GPU-BSM -m 5 –e2e -l 1 -R -d C-CGG, GPU-BSM -m 5 -l 1 -R -d C-CGG; moreover for all experiments with GPU-BSM the following setting has been used: -L 100 -g 0 to run the experiment on a single GPU (-L 100 -g 0 -g 1 to run the experiment on two GPUs); ii) Bismark -q –directional, Bismark -q –directional –bowtie2 -p 6; iii) BSMAP -v 5 -w 2 -r 0 -D -C-CGG -p 12; iv) BS-Seeker2 -m 5 –aligner = bowtie -f sam -r -c C-CGG -L 40 -U 220, BS-Seeker2 -m 5 –aligner = bowtie2 -f sam -r -c C-CGG -L 40 -U 220 –bt2–end-to-end –bt2-p 6, BS-Seeker2 -m 5 –aligner = bowtie2 -f sam -r -c C-CGG -L 40 -U 220 –bt2-p 6.
GPU-BSM run on a single GPU.
GPU-BSM run on two GPUs.
Bismark and BS-Seeker2 run in parallel two instances of Bowtie2. To ensure that both tools use 12 core we used the option -p 6/–bt2-p 6 so that each Bowtie2 instance runs with 6 threads.