Table 1 SPUMONI index measurements when built over 500 E. coli strains (total size 2.5 GB) using different minimizer schemes and alphabets. Both minimizer schemes used a small window size (k) of 4. The forward and reverse complement for each E. coli genome was included in the index
From: SPUMONI 2: improved classification using a pangenome index of minimizer digests
w | No digestion | \(\boldsymbol w\boldsymbol=\mathbf8\) | \(\boldsymbol w\boldsymbol=\mathbf{16}\) | ||
|---|---|---|---|---|---|
Alphabet | Minimizer | DNA | Minimizer | DNA | |
n | 5.13 billion | 1.61 billion | 6.78 billion | 663 million | 2.85 billion |
r | 65.2 million | 31.8 million | 64.4 million | 17.5 million | 35.1 million |
n/r | 78.753 | 50.603 | 105.35 | 37.888 | 81.251 |
Index size | 232 MB | 142 MB | 227 MB | 73 MB | 124 MB |