Table 6 Read cloud deconvolution specifically promotes reads to low taxonomic ranks such as genus and species in the MOCK5 LoopSeq dataset. The column “Promotion” indicates the promotion of a paired read i from initial rank X to rank Y as “X\(\rightarrow\)Y” using deconvolved read cloud information. The abbreviations are as follows: root (R), kingdom/domain (D), phylum (P), class (C), order (O), family (F), genus (G), species (S). The columns “Prop. Improvement” are calculated by taking the difference between the number of reads promoted using the enhanced read clouds and the number of reads promoted using the original read clouds, divided by the latter
From: Ariadne: synthetic long read deconvolution using assembly graphs
Promotion | No Deconv. | Reference | Prop. Improvement | Ariadne | Prop. Improvement |
|---|---|---|---|---|---|
R\(\rightarrow\)D | 218728 | 46849 | − 0.786 | 48874 | − 0.777 |
R\(\rightarrow\)P | 17279 | 22947 | 0.328 | 29216 | 0.691 |
R\(\rightarrow\)C | 751 | 3132 | 3.17 | 4950 | 5.591 |
R\(\rightarrow\)O | 52 | 238 | 3.577 | 211 | 3.058 |
R\(\rightarrow\)F | 4416 | 109025 | 23.689 | 102446 | 22.199 |
R\(\rightarrow\)G | 732 | 40611 | 54.48 | 38472 | 51.557 |
R\(\rightarrow\)S | 873 | 21840 | 24.017 | 20214 | 22.155 |
D\(\rightarrow\)P | 43418 | 57680 | 0.328 | 62255 | 0.434 |
D\(\rightarrow\)C | 1432 | 12935 | 8.033 | 6045 | 3.221 |
D\(\rightarrow\)O | 314 | 1268 | 3.038 | 693 | 1.207 |
D\(\rightarrow\)F | 8729 | 257083 | 28.452 | 185629 | 20.266 |
D\(\rightarrow\)G | 661 | 35883 | 53.286 | 21612 | 31.696 |
D\(\rightarrow\)S | 5044 | 159161 | 30.555 | 82228 | 15.302 |
P\(\rightarrow\)C | 2919 | 5012 | 0.717 | 5263 | 0.803 |
P\(\rightarrow\)O | 173 | 695 | 3.017 | 246 | 0.422 |
P\(\rightarrow\)F | 4250 | 58696 | 12.811 | 52537 | 11.362 |
P\(\rightarrow\)G | 1477 | 27221 | 17.43 | 21011 | 13.225 |
P\(\rightarrow\)S | 17901 | 137048 | 6.656 | 123977 | 5.926 |
C\(\rightarrow\)O | 1433 | 1390 | − 0.03 | 642 | − 0.552 |
C\(\rightarrow\)F | 42320 | 82915 | 0.959 | 81462 | 0.925 |
C\(\rightarrow\)G | 10177 | 28636 | 1.814 | 25441 | 1.5 |
C\(\rightarrow\)S | 362453 | 376538 | 0.039 | 379622 | 0.047 |
O\(\rightarrow\)F | 374749 | 374638 | − 0.0 | 372959 | − 0.005 |
O\(\rightarrow\)G | 62752 | 60838 | − 0.031 | 60382 | − 0.038 |
O\(\rightarrow\)S | 691071 | 694087 | 0.004 | 699056 | 0.012 |
F\(\rightarrow\)G | 1096859 | 1092951 | − 0.004 | 1094013 | − 0.003 |
F\(\rightarrow\)S | 1354793 | 1360920 | 0.005 | 1365901 | 0.008 |
G\(\rightarrow\)S | 1957897 | 1962799 | 0.003 | 1966810 | 0.005 |