Table 1.
Statistics for the different mappers with mouse chromosome 1 simulation data
| Algorithm | Library | Mode | Mapping percentage | True Positive rate | Memory in gbytes | Running Time in minutes | Output size in Mbytes |
|---|---|---|---|---|---|---|---|
| bowtie | PE | unique | 91.87823 | 99.97913 | 0.92 | 3.00 | 583.36 |
| bowtie | SE | unique | 92.05224 | 99.92287 | 0.69 | 1.33 | 311.38 |
| bowtie2 | PE | unique | 94.57886 | 99.93802 | 1.28 | 38.00 | 572.58 |
| bowtie2 | SE | unique | 92.08282 | 99.84845 | 1.18 | 32.67 | 294.64 |
| Bwa aln | PE | unique | 94.62602 | 99.88782 | 2.66 | 15.67 | 553.86 |
| Bwa aln | SE | unique | 96.60879 | 95.82612 | 1.85 | 3.00 | 310.30 |
| Bwa mem | PE | unique | 94.54763 | 99.95728 | 8.77 | 19.33 | 563.50 |
| Bwa mem | SE | unique | 92.08548 | 99.89624 | 8.40 | 4.67 | 299.76 |
| novoalign | PE | unique | 95.55760 | 99.61473 | 7.62 | 226.33 | 609.08 |
| novoalign | SE | unique | 92.08982 | 99.92307 | 7.61 | 31.67 | 315.96 |
| STAR | PE | unique | 95.37882 | 99.80753 | 16.67 | 2.00 | 553.24 |
| STAR | SE | unique | 92.23340 | 99.73004 | 16.18 | 2.33 | 285.06 |
| bowtie | PE | random | 99.95300 | 93.67212 | 0.93 | 3.00 | 596.75 |
| bowtie | SE | random | 99.99001 | 93.04126 | 0.69 | 2.33 | 317.67 |
| bowtie2 | PE | random | 99.99991 | 95.89737 | 1.28 | 35.67 | 607.86 |
| bowtie2 | SE | random | 99.98093 | 92.97406 | 1.18 | 25.67 | 324.26 |
| Bwa aln | PE | random | 99.99998 | 95.94218 | 2.66 | 17.67 | 604.39 |
| Bwa aln | SE | random | 99.99801 | 93.01531 | 1.85 | 4.00 | 322.33 |
| Bwa mem | PE | random | 99.99998 | 95.94068 | 9.42 | 18.33 | 612.39 |
| Bwa mem | SE | random | 99.99998 | 93.01096 | 7.96 | 6.33 | 329.82 |
| novoalign | PE | random | 99.99998 | 95.84899 | 7.62 | 272.00 | 616.78 |
| novoalign | SE | random | 99.99989 | 93.03697 | 7.61 | 30.67 | 322.72 |
| STAR | PE | random | 99.94380 | 95.93094 | 16.67 | 5.00 | 583.02 |
| STAR | SE | random | 99.99024 | 93.01921 | 16.26 | 2.00 | 314.19 |
| bowtie | PE | multi | 99.95300 | 92.89719 | 0.98 | 18.33 | 7289.52 |
| bowtie | SE | multi | 99.99001 | 93.01711 | 0.71 | 9.67 | 2747.64 |
| bowtie2 | PE | multi | 99.99998 | 76.80653 | 11.53 | 28658.67 | 228148.51 |
| bowtie2 | SE | multi | 99.99998 | 70.81391 | 8.74 | 8205.33 | 161697.48 |
| novoalign | PE | multi | 99.99998 | 95.85903 | 7.62 | 307.67 | 2627.41 |
| novoalign | SE | multi | 99.99989 | 93.03718 | 7.61 | 99.00 | 3176.37 |
| STAR | PE | multi | 99.94380 | 95.93265 | 23.95 | 7.00 | 2575.59 |
| STAR | SE | multi | 99.99024 | 93.02143 | 26.64 | 4.00 | 2831.57 |
Values correspond to the average values of three independent simulated libraries with a 10X coverage. SE and PE refer to single end and paired end, respectively. Post-mapping filtering were applied for Bowtie2, Bwa mem and aln algorithms in order to extract uniquely-mapped reads