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Merge pull request #57 from genomehubs/2023.08.23
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2023.08.23
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@ccaio
ccaio authored Aug 24, 2023
2 parents 7219010 + 5cab025 commit 667022b
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Showing 108 changed files with 39,024 additions and 37,252 deletions.
Binary file modified sources/assembly-data-sample/ncbi_datasets_eukaryota_sample.tsv.gz
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8 changes: 8 additions & 0 deletions sources/genomesize_karyotype/DTOL_Plant_Genome_Size_Estimates.tsv
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Expand Up @@ -1560,3 +1560,11 @@ RBGE DMR377 DTOL Angiosperm Onagraceae Epilobium palustre <Oryza GPB3%PVP 144.42
RBGE DMR378 DTOL Angiosperm Asteraceae Cicerbita macrophylla >Petro GPB3%PVP 179.37 452.21 3.37 3.27 2.521 455.64 181.99 11.34 11.27 5.63 5.51 3.35 3.4 0.021 0.097 Nacho 17/08/2023 NA NA NA NA NA 1
RBGE DMR379 DTOL Angiosperm Fabaceae Lotus pedunculatus <Solanum GPB3%PVP 191.67 314.76 5.44 4.14 1.642 190.75 364.92 1.21 1.2 0.6 0.59 4.8 3.85 0.482 0.006 Nacho 17/08/2023 NA 2C = 0.78pg NA NA NA 1
RBGE DMR380 DTOL Angiosperm Malvaceae Malva neglecta <Solanum GPB3%PVP 177.66 258.55 6.48 4.84 1.455 178.97 271.3 1.36 1.37 0.68 0.67 5.8 4.57 0.123 0.013 Nacho 17/08/2023 NA 2C = 1.60pg Young stamens (2C). ca. 400 nuclei... rough estimate NA NA 1
RBGE DMR381 DTOL Angiosperm NA Scrophularia umbrosa NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1
RBGE DMR382 DTOL Angiosperm NA Mentha spicata NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1
RBGE DMR383 DTOL Angiosperm NA Galeopsis bifida NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1
RBGE DMR384 DTOL Angiosperm NA Scirpus sylvaticus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1
RBGE DMR385 DTOL Angiosperm NA Potamogeton obtusifolius NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1
RBGE DMR386 DTOL Angiosperm NA Epilobium ciliatum NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1
RBGE DMR387 DTOL Angiosperm NA Persicaria nepalensis NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1
RBGE DMR388 DTOL Angiosperm NA Glebionis segetum NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1
205 changes: 105 additions & 100 deletions sources/genomesize_karyotype/DTOL_assembly_informatics_status_kmer_draft.tsv
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Expand Up @@ -4,9 +4,6 @@ taxon est_size_mb length_mb
78070 34 38
49291 240 265
59425 894 850
220392 2091 1493
56720 685 769
39082 2407 2498
7153 183 186
268694 690 695
268641 606 587
Expand Down Expand Up @@ -209,7 +206,6 @@ taxon est_size_mb length_mb
173286 244 219
195075 623 729
295815 568 540
28680 1084 1192
443705 1530 1096
9731 2740 2662
70193 5192 5811
Expand All @@ -227,12 +223,6 @@ taxon est_size_mb length_mb
1100902 606 622
6550 1272 1623
110926 1115 1281
34570 4115 5074
136194 188 190
2561093 421 462
346772 790 785
1352472 789 768
934957 321 367
243486 5235 5580
82655 985 1136
61751 2663 2740
Expand All @@ -253,15 +243,24 @@ taxon est_size_mb length_mb
203779 579 547
27771 601 718
364141 411 488
28680 1084 1192
34570 4115 5074
136194 188 190
2561093 421 462
346772 790 785
1352472 789 768
934957 321 367
2822767 61 57
230827 59 63
997532 802 800
1774267 735 835
331320 411 441
471023 329 332
206348 2190 2045
304530 485 626
331350 477 565
345037 354 360
471055 413 441
97307 518 462
157641 244 330
206348 2190 2045
23211 520 490
311941 324 572
331329 630 723
331327 539 536
344637 656 739
Expand All @@ -276,7 +275,6 @@ taxon est_size_mb length_mb
81636 374 NA
37639 8925 11850
116142 8276 15065
223681 216 244
1587122 462 453
1667470 307 401
1603211 170 115
Expand All @@ -286,11 +284,9 @@ taxon est_size_mb length_mb
2881813 549 528
1779456 124 302
709496 44 47
2822767 61 319
2447973 40 284
1101044 782 792
318605 61 67
230827 59 NA
557324 87 118
440096 51 294
378274 58 1
Expand All @@ -308,118 +304,127 @@ taxon est_size_mb length_mb
133487 25 23
63597 25 109
173376 205 140
41496 739 1186
1000418 783 943
119177 1696 3310
13597 1580 1408
1053398 268 483
50459 306 230
3710 455 455
50462 230 209
311941 324 572
212925 1236 1010
1053368 414 569
65948 317 227
1149847 373 387
172267 374 439
77065 405 404
39468 786 796
15000 9559 NA
83862 719 681
298643 724 654
57933 575 587
23211 520 490
15000 9559 9379
114204 346 404
15193 2058 315
372271 394 417
234464 444 433
312760 412 363
241230 403 389
241234 433 365
316510 591 584
234466 375 356
223681 216 244
240680 449 390
312760 412 363
457147 542 518
59985 285 803
164258 394 338
191669 274 399
65561 397 402
544475 371 334
114206 581 551
398450 196 335
313220 280 244
13487 623 NA
42036 2577 2134
415813 518 460
91168 425 306
55501 1063 956
291096 759 690
56853 975 817
644184 378 655
767568 476 457
53178 1040 877
702255 281 530
169223 3597 3323
53164 654 594
318445 325 310
127129 644 NA
13129 717 NA
1060938 485 640
165318 NA 755
3882 581 719
114937 249 379
169241 921 491
38787 375 490
376124 3238 2865
32247 286 243
41653 1074 2099
113538 11594 NA
126913 436 839
487684 931 1029
75704 739 814
4166 559 432
165094 552 1093
76438 342 390
475394 484 659
756629 772 693
13805 414 1057
374711 275 548
60093 783 673
3580 363 717
125585 1413 1672
234471 310 338
241234 433 365
372271 394 417
241200 406 NA
241200 363 NA
15193 2058 315
234464 444 NA
241230 403 389
487684 931 1029
77065 405 404
172267 374 439
1149847 373 387
75704 739 814
220462 8810 18725
128002 4672 3725
210355 348 238
475394 484 659
154990 452 603
756629 772 693
212925 1236 1010
4039 485 468
193516 1225 1011
4166 559 432
41496 739 1186
114204 346 404
29818 755 606
457147 542 518
97307 518 462
157641 244 330
94688 192 1098
13805 414 1057
702255 281 530
3905 2582 NA
69996 147 336
69996 255 260
75065 315 NA
41492 1717 800
4123 1310 1066
186058 482 591
119177 1696 3310
53159 830 800
374711 275 548
13597 1580 1408
1060938 485 640
41653 1074 2099
165318 NA 755
60093 783 673
3580 363 717
169223 3597 3323
313220 280 244
291096 759 690
230724 461 476
1053398 268 483
191669 274 399
126913 436 839
169241 921 491
125585 1413 1672
50459 306 230
3710 455 455
50462 230 209
65561 397 402
1053368 414 569
65948 317 227
109996 525 532
415813 518 460
59985 285 803
38787 375 490
1053350 547 281
56853 975 817
83862 719 681
173702 763 695
298643 724 654
238501 891 999
379949 353 425
99497 856 631
313096 5389 5860
3882 581 719
544475 371 334
644184 378 655
114937 249 379
32247 286 243
1534653 2629 2698
91168 425 306
347188 3549 2728
114206 581 551
55501 1063 956
29664 393 379
376124 3238 2865
76455 564 514
318445 325 310
165094 552 1093
316508 359 548
316510 591 584
53178 1040 877
127129 644 NA
13129 717 NA
39879 2495 NA
76438 342 390
137095 1671 NA
1000418 783 943
164258 394 338
398450 196 335
254778 548 NA
767568 476 457
113538 11594 NA
63632 1362 NA
13487 623 NA
42036 2577 2134
57933 575 587
82213 5202 6120
175095 1066 2681
48027 1846 NA
1088609 319 555
2884248 342 405
1889570 201 218
Expand Down Expand Up @@ -483,14 +488,12 @@ taxon est_size_mb length_mb
948063 2625 3419
8324 22479 24777
2576622 593 643
82213 5202 NA
175095 1066 2680
53164 654 594
997532 802 812
1774267 735 NA
331320 411 NA
1545128 1024 1016
471023 329 NA
197171 2102 2117
988087 742 NA
27393 2321 4750
987919 846 NA
446505 1518 2920
2591979 1722 NA
97200 3701 NA
52573 1229 NA
Expand All @@ -505,6 +508,10 @@ taxon est_size_mb length_mb
55710 815 NA
55774 3200 NA
1090477 1400 NA
278673 1339 NA
2980199 2 NA
2980188 825 NA
88953 440 NA
2054275 81 80
322858 404 984
6082 1 NA
Expand Down Expand Up @@ -674,7 +681,6 @@ taxon est_size_mb length_mb
753150 871 NA
1594228 559 NA
242269 856 NA
988087 739 NA
987445 1162 NA
683962 327 NA
1070333 351 NA
Expand Down Expand Up @@ -1126,7 +1132,6 @@ taxon est_size_mb length_mb
75960 1863 NA
202021 1454 NA
878349 522 NA
446505 1896 NA
1436830 808 NA
1101111 1206 NA
1870097 666 NA
Expand Down
2 changes: 1 addition & 1 deletion sources/genomesize_karyotype/FILE_DTOL_Plant_Genome_Size_Estimates.types.yaml
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Expand Up @@ -3,7 +3,7 @@ file:
header: true
name: DTOL_Plant_Genome_Size_Estimates.tsv
source: DTOL Plant Genome Estimates Kew
source_date: 2023-08-22
source_date: 2023-08-23
attributes:
genome_size:
type: long
Expand Down
2 changes: 1 addition & 1 deletion sources/genomesize_karyotype/FILE_DTOL_assembly_informatics_status_kmer_draft.types.yaml
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Expand Up @@ -3,7 +3,7 @@ file:
header: true
name: DTOL_assembly_informatics_status_kmer_draft.tsv
source: Darwin Tree of Life Assembly Team
source_date: 2023-08-22
source_date: 2023-08-23
source_url: https://qc.tol.sanger.ac.uk/
attributes:
genome_size_kmer:
Expand Down
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