Table 4 Percentage of reads aligned in S1 and S2 data sets by four aligners under different settings
S1 | S2 | ||||
|---|---|---|---|---|---|
w/o trim | w/trim | w/o trim | w/trim | ||
7,406,247 | 7,006,805 | 5,398,566 | 5,193,655 | ||
Randomly report one alignment per read | SOAP2 | 75.96% | 91.45% | 42.12% | 76.81% |
Bowtie | 75.71% | 91.36% | 41.83% | 76.67% | |
BWA | 76.12% | 91.80% | 41.94% | 76.88% | |
Novoalign | 73.64% | 91.60% | 34.50% | 76.94% | |
Suppress reads w/ multiple alignments | SOAP2 | 71.85% | 85.90% | 39.75% | 71.31% |
Bowtie | 68.82% | 81.90% | 38.89% | 68.63% | |
BWA | 74.40% | 84.07% | 39.12% | 69.75% | |
Novoalign | 69.67% | 86.09% | 32.63% | 71.63% | |