Table 2 Rabema benchmarking results for mapping 100k simulated reads of length 100 bps to hg19
From: Fast and efficient short read mapping based on a succinct hash index
Mappers | Mapped | Accuracy \(\left (\begin {array}{ll} & \text {ED 0 ED 1 ED 2} \\[-10pt] \text {total} & \\[-10pt] & \text {ED 3 ED 4}\\ \end {array}\right)\) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
reads | All[%] | All-best[%] | Any-best[%] | ||||||||||
FEM-vl | 99997 | 100.00 | 100.0 | 100.0 | 100.0 | 100.00 | 100.0 | 100.0 | 100.0 | 100.00 | 100.0 | 100.0 | 100.0 |
100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | ||||||||
FEM-g | 99997 | 99.9705 | 100.0 | 100.0 | 100.0 | 100.00 | 100.0 | 100.0 | 100.0 | 100.00 | 100.0 | 100.0 | 100.0 |
99.99 | 99.25 | 100.0 | 100.0 | 100.0 | 100.0 | ||||||||
Hobbes3 | 99997 | 100.00 | 100.0 | 100.0 | 100.0 | 100.00 | 100.0 | 100.0 | 100.0 | 100.00 | 100.0 | 100.0 | 100.0 |
100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | ||||||||
BitMapper | 99997 | 99.9999 | 100.0 | 100.0 | 100.0 | 100.00 | 100.0 | 100.0 | 100.0 | 100.00 | 100.0 | 100.0 | 100.0 |
100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | ||||||||
BitMapper2 | 99997 | 99.9998 | 100.0 | 100.0 | 100.0 | 100.00 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 |
100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | ||||||||
Masai | 99995 | 99.9493 | 100.0 | 100.0 | 100.0 | 99.998 | 100.0 | 100.0 | 100.0 | 99.998 | 100.0 | 100.0 | 100.0 |
99.97 | 98.73 | 100.0 | 97.33 | 100.0 | 97.33 | ||||||||
GEM | 99994 | 98.6008 | 100.0 | 99.99 | 99.80 | 99.994 | 100.0 | 99.99 | 99.98 | 99.997 | 100.0 | 100.0 | 100.0 |
89.97 | 70.24 | 100.0 | 96.00 | 100.0 | 96.00 | ||||||||
BWA | 99990 | 92.2433 | 98.66 | 96.79 | 85.80 | 97.5195 | 97.46 | 97.70 | 97.35 | 99.985 | 100.0 | 99.97 | 99.93 |
36.11 | 1.83 | 98.03 | 96.15 | 99.74 | 97.33 | ||||||||