Table 2 Comparative analysis of read elongation tools.
From: Konnector v2.0: pseudo-long reads from paired-end sequencing data
Running time (hms) | Peak memory (MB) | N50 (bp) | Misassembled Reads Length (bp) | Percent genome coverage | |
|---|---|---|---|---|---|
E. coli (synthetic) | |||||
ELOPER | 10m46s | 19013 | 501 | 16146 | 100.00 |
GapFiller | 32m39s | 476 | 396 | 14103 | 100.00 |
MaSuRCA super-reads | 2m56s | 4669 | 54103 | 0 | 100.00 |
Konnector (k = 50) | 6m15s | 81 | 406 | 3133 | 100.00 |
Konnector 2 (k = 70) | 5m0s | 100 | 32012 | 276 | 99.99 |
S. cerevisiae | |||||
ELOPER | 97h55m23s | 37119 | 144 | 71426 | 99.32 |
GapFiller | 3h13m18s | 666 | 332 | 96869 | 97.04 |
MaSuRCA super-reads | 4m2s | 5294 | 1684 | 129828 | 98.67 |
Konnector (k = 50) | 8m34s | 231 | 315 | 75435 | 97.94 |
Konnector 2 (k = 40) | 7m1s | 232 | 4690 | 67505 | 98.99 |
C. elegans | |||||
ELOPER | exceeds available memory (120GB) | ||||
GapFiller | exceeds available memory (120GB) | ||||
MaSuRCA super-reads | 2h2m17s | 80742 | 2554 | 1925740 | 99.98 |
Konnector (k = 55) | 5h5m21s | 1954 | 475 | NA | 99.80 |
Konnector 2 (k = 80) | 3h30m23s | 2193 | 6232 | 837480 | 99.88 |
H. sapiens (NA19238) | |||||
ELOPER | not attempted | ||||
GapFiller | not attempted | ||||
MaSuRCA super-reads | exceeds available memory (120 GB) | ||||
Konnector (k = 150) | 4d9h15m48s | 410381 | 556 | NA | 94.15 |
Konnector 2 (k = 180) | 20h47m24s | 471905 | 3051 | NA | 94.01 |