Table 6 Impact of suffix array compression Suffix array memory requirements for various suffix array compression ratios (target length = 1 billion), and the time taken to locate() 1 million length-14 nucleotide queries for in-memory and on-disk suffix arrays
From: An optimized FM-index library for nucleotide and amino acid search
Suffix array | Locate() time (s) | |||
|---|---|---|---|---|
Compression ratio | Suffix array size | In-memory SA | SSD SA | HDD SA |
1 | 3750 MB | 0.67 | 2.18 | 8.71 |
2 | 1875 MB | 1.28 | 3.44 | 6.18 |
4 | 938 MB | 2.41 | 4.75 | 6.64 |
8 | 469 MB | 4.72 | 6.98 | 8.40 |
16 | 234 MB | 9.42 | 12.34 | 11.98 |
32 | 117 MB | 19.00 | 20.66 | 21.10 |
64 | 59 MB | 37.07 | 39.42 | 39.58 |
128 | 29 MB | 75.25 | 77.14 | 79.25 |