Table 2 Alignment performance benchmarks on GTDB complete dataset
From: Efficient sequence alignment against millions of prokaryotic genomes with LexicMap
Query (length) | Tool | Hits (total) | Hits (high) | Hits (medium) | Hits (low) | Time | RAM |
|---|---|---|---|---|---|---|---|
A rare gene 1,299 bp | LexicMap | 6,255 | 2,311 | 46 | 3,898 | 30 s | 2.1 GB |
BLASTn | 7,121 | 2,311 | 47 | 4,763 | 2,171 s | 351.2 GB | |
BLASTn (ws = 15) | 57,741 | 2,311 | 47 | 55,383 | 3,171 s | 324.1 GB | |
MMseqs2 | 67,537 | 2,304 | 54 | 65,179 | 26,174 s | 400.7 GB | |
Minimap2 | 2,312 | 2,312 | 0 | 0 | 17,208 s | 20.2 GB | |
A 16S rRNA gene 1,542 bp | LexicMap | 306,064 | 60,999 | 69,293 | 175,772 | 303 s | 5.2 GB |
BLASTn | 301,197 | 61,878 | 109,477 | 129,842 | 2,760 s | 378.4 GB | |
BLASTn (ws = 15) | 301,197 | 61,878 | 109,477 | 129,842 | 3,291 s | 378.4 GB | |
MMseqs2 | 324,364 | 60,915 | 89,874 | 173,575 | 31,140 s | 400.7 GB | |
Minimap2 | 17,656 | 15,998 | 1,652 | 6 | 17,313 s | 20.2 GB | |
A plasmid 52,830 bp | LexicMap | 65,029 | 21 | 2,808 | 62,200 | 539 s | 6.8 GB |
BLASTn | 69,311 | 21 | 2,865 | 66,425 | 2,262 s | 364.7 GB | |
BLASTn (ws = 15) | 91,847 | 21 | 2,865 | 88,961 | 3,082 s | 142.8 GB | |
MMseqs2 | 90,277 | 7 | 1,650 | 88,620 | 44,710 s | 400.7 GB | |
Minimap2 | 3,033 | 35 | 1,873 | 1,125 | 19,715 s | 20.2 GB | |
1,033 AMR genes 1 kb (median) | LexicMap | 4,665,317 | 1,123,251 | 776,153 | 2,765,913 | 8,620 s | 10.7 GB |
BLASTn | 5,357,772 | 1,150,407 | 772,858 | 3,434,507 | 4,686 s | 442.1 GB | |
BLASTn (ws = 15) | 10,877,544 | 1,150,410 | 840,464 | 8,886,670 | 4,561 s | 311.9 GB | |
MMseqs2 | 10,137,345 | 1,148,942 | 808,177 | 8,180,226 | 184,470 s | 406.9 GB | |
Minimap2 | 2,078,490 | 943,516 | 39,529 | 815,445 | 38,058 s | 20.2 GB |
