Table 3 Running time and memory usage for indexing and querying a de Bruijn graph for 30 million short reads
From: Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
Tool | Process | Time (m) | Memory (GB) |
|---|---|---|---|
Bifrost | Build | 333 | 39.6 |
Index | 11.1 | 26.8 | |
Query | 4.7 | 26.8 | |
Query-total | 16.4 | 26.8 | |
BCALM2 | Build | 380 | 35.58 |
Blight | Index | 80 | 8.3 |
Query | 13.6 | 8.3 | |
Query-total | 93.6 | 8.3 | |
Squeakr | Build | 1147 | 80 |
Mantis | Index | 54 | 17 |
Query | 38.8 | 168 | |
Query-total | 96.9 | 168 |