Table 8 Comparison of Nexus (\(s_{\textrm{SA}} = 16\)) with other indexes that support read alignment either to a linear index (BWA, Bowtie 2), or to a graph which is used as a reference (Giraffe, deBGA, Pufferfish, A4)
From: Pan-genome de Bruijn graph using the bidirectional FM-index
Tool | Pan-genome representation | Memory usage data structure (GiB) | Construction time | Construction peak RAM usage (GiB) |
|---|---|---|---|---|
deBGA | dBG | 90.50 | 10 hours and 9 minutes | 312.13 |
Pufferfish | ccdBG | 62.29 | 17 hours and 27 minutes | 139.24 |
A4 | ccdBG | 36.91 | 7 hours and 22 minutes | 38.77 |
BWA | Linear concatenation | 49.45 | 13 hours and 47 minutes | 42.40 |
Bowtie 2 | Linear concatenation | 54.14 | 26 hours | 246.88 |
Giraffe | Variation graph | 180.04 | 21 hours and 3 minutes | 638.93 |
Nexus | ccdBG | 95.46 | 15 hours and 44 minutes | 269.32 |