Table 2 Benchmarking results of de novo and genome-guided transcriptome assembly for plant RiPP precursor discovery
Assembler | Approach | Total time [min] | Total memory usage [GB] | Total detected cores (98 total cores) | Detected unique correct cores (38 total unique cores) | Detected repetitive cores (87 total repetitive cores) | Similarity [sum %] (total similarity score: 2000) | Identity [sum %] (total identity score: 2000) |
|---|---|---|---|---|---|---|---|---|
MEGAHIT (v1.2.9) | De novo | 940 ± 44 | 123 ± 1 | 42 ± 0 | 24 ± 0 | 32 ± 0 | 1582 ± 0 | 1587 ± 0 |
SPAdes (v3.15.5) | De novo | 1185 ± 39 | 180 ± 1 | 66 ± 0 | 32 ± 0 | 56 ± 0 | 1728 ± 0 | 1713 ± 0 |
Trinity (v2.15.1) | De novo | 13683 ± 621 | 485 ± 6 | 41 ± 0 | 25 ± 0 | 30 ± 1 | 1527 ± 2 | 1521 ± 2 |
StringTie (v2.2.1) | Genome-guided | 922 ± 621 | 1635 ± 2 | 77 ± 0 | 27 ± 0 | 65 ± 0 | 1565 ± 0 | 1545 ± 0 |
Trinity (v2.15.1) | Genome-guided | 10545 ± 417 | 1787 ± 4 | 62 ± 0 | 28 ± 0 | 51 ± 0 | 1795 ± 1 | 1691 ± 1 |
