Table 2.
Performance comparison of software packages for locus-specific analysis of bisulfite sequencing data
| Region | Read count | Performance |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| BiQ Analyzer 2.0 |
QUMAa |
BiQ Analyzer HT |
BiQ Analyzer HTb |
||||||
| Memory | ET | Memory | ET | Memory | ET | Memory | ET | ||
| RE1 | 400 | 350 | 300 | NAc | 10 | 95 | 30 | 1000 | 6 |
| RE2 | 1054 | 500 | 911 | NAc | 25 | 200 | 50 | 1000 | 9 |
| RE3 | 3150 | >1000 | 3455 | NAc | 70 | 200 | 95 | 1000 | 16 |
| RE3d | 10 000 | NAe | NAc | 323 | 300 | 285 | 1500 | 50 | |
| RE3d | 100 000 | NAe | NAf | NAg | 3500 | 440 | |||
| RE3d | 1 000 000 | NAe | NAf | NAg | 10 000 | 1940 | |||
All tests, except for the cases noted explicitly, were run on a standard laptop with dual-core processor and 2 GB main memory. The values of peak memory usage are given in MB. ET (‘execution time’) denotes the total duration of the analysis in seconds.
aThe QUMA web-server running on a high-performance machine (8 dual-core processors, 16 GB main memory).
bBiQ Analyzer HT running on a high-performance machine (8 dual-core processors, 16 GB main memory).
cMemory usage of the web-server does not affect performance for the end user.
dThe data set was obtained by concatenating multiple copies of the initial set of reads obtained for RE3.
eThe calculation could not be finished due to an error.
fThe calculation failed because it exceeded the web-server's maximum read threshold.
gTests with BiQ Analyzer HT for the last two read sets were performed only on the high-performance computer.