Mapper
|
Index type
|
Adjustable
|
Size on disk
|
Peak memory
|
Construction time
|
|---|
| | | |
(GB)
|
(GB)
|
(h:mm)
|
|---|
ALFALFA (s=4) | ESSA | yes | 10.7 | 11.0 | 0:19 |
ALFALFA (s=12) | ESSA | yes | 5.6 | 5.7 | 0:10 |
Bowtie 2 | FM-index | yes | 3.9 | 5.3 | 1:58 |
BWA | FM-index | no | 5.2 | 5.4 | 1:18 |
CUSHAW3 | FM-index | no | 3.7 | 3.5 | 0:36 |
GEM | FM-index | yes | 4.8 | 5.0 | N.A. §
|
- The ALFALFA index is evaluated for two different sparseness values. The read mappers BWA-SW and BWA-MEM both use the same index structure, jointly reported as BWA. The third column indicates whether memory footprint can be tuned via user-specified options. The fourth column reports the memory footprint of the index structure when stored on disk. The fifth column provides peak memory of the read mapper observed during alignment of 1kbp reads. The time needed to construct the index structure is given in the last column. §A pre-built GEM index was downloaded from the GEM website as the indexer of this mapper ran into a fatal error in our test environment.
