Table 1 Summary statistics of aligning PacBio/ONT reads to short-read assembly graphs (constructed by SPAdes with kmer size equal to 77)
From: SPAligner: alignment of long diverged molecular sequences to assembly graphs
Aligner | MR(%) | AI (%) | T (h:m) | M (Gb) | MR(%) | AI (%) | T (h:m) | M (Gb) | |
|---|---|---|---|---|---|---|---|---|---|
E. coli PacBio | E. coli ONT | ||||||||
vg | 29 | 90 | 00:41 | 4.1 | 58 | 88 | 00:33 | 3.3 | |
GraphAligner | 85.3 | 86.7 | 00:01 | 0.1 | 82.2 | 86.1 | 00:01 | 0.2 | |
GA try-all-seeds | 86 | 86.6 | 00:25 | 0.3 | 83.6 | 86 | 01:43 | 4.8 | |
SPAligner | 88.3 | 86.5 | 00:04 | 0.3 | 86.6 | 86.1 | 00:03 | 0.3 | |
S. cerevisiae PacBio | S. cerevisiae ONT | ||||||||
vg | 15 | 90 | 28:03 | 91 | 70 | 47 | 42:59 | 85 | |
GraphAligner | 53.7 | 86.5 | 00:01 | 0.2 | 65.7 | 81.1 | 00:01 | 0.2 | |
SPAligner | 56.5 | 85.9 | 00:38 | 0.7 | 61.6 | 82.1 | 00:16 | 0.6 | |
C. elegans PacBio | C. elegans ONT | ||||||||
vg | 10 | 91 | 76:26 | 306 | 15 | 89 | 60:58 | 309 | |
GraphAligner | 84.1 | 86.8 | 00:03 | 1.8 | 63.6 | 86.6 | 00:03 | 1.8 | |
SPAligner | 84.6 | 86.5 | 01:06 | 1.2 | 66 | 86.4 | 00:34 | 1.3 | |