Runtime and Memory Consumption of the Study Projects Using an Intel 2.4 GHz Xeon P4/HT PC With 512 K L2 Cache and 2 G RDRAM
|
|
Sponge |
Dog |
Grapevine |
|---|---|---|---|
| Peak memory usage | 250 M | 280 M | 1.7 G |
| Runtime in minutes | |||
| Step 1 | 27 | 14 | 735 |
| Step 2 | 20 | 10 | 101 |
| Step 3 | 3 | 4 | 35 |
| Total | 137 | 69 | 871 |
| Number of contig reassemblies | |||
| Step 1 | 577 | 250 | 3827 |
| Step 2 | 51 | 18 | 1927 |
| Step 3 | 0 | 0 | 0 |
| Total reassemblies
|
628
|
268
|
5754
|
-
Comparison of the sponge and dog project, which have roughly the same number of sequences showing a clear relationship between the runtime and the number of detected contig reassemblies (which were triggered by newly detected SNP sites).
The reduced runtime from step 1 to step 2 is due to potentially problematic regions with SNP sites that were detected in the first step. These SNPs give additional information to the second step, which then prevents misassemblies that involve those sites. Hence, the lower number of reassemblies reduced runtime.
In general, step 3 has less transcript sequences to assemble than step 1 and step 2, also leading to reduced runtimes.
