---------------- Information for assembly 'p_ctg.fa' ----------------
Number of scaffolds 2968
Total size of scaffolds 185941456
Longest scaffold 1175772
Shortest scaffold 56
Number of scaffolds > 1K nt 2937 99.0%
Number of scaffolds > 10K nt 2346 79.0%
Number of scaffolds > 100K nt 486 16.4%
Number of scaffolds > 1M nt 4 0.1%
Number of scaffolds > 10M nt 0 0.0%
Mean scaffold size 62649
Median scaffold size 23092
N50 scaffold length 166627
L50 scaffold count 273
n90 scaffold length 23705
L90 scaffold count 1451
scaffold %A 31.52
scaffold %C 18.42
scaffold %G 18.45
scaffold %T 31.61
scaffold %N 0.00
scaffold %non-ACGTN 0.00
Number of scaffold non-ACGTN nt 0
Percentage of assembly in scaffolded contigs 0.0%
Percentage of assembly in unscaffolded contigs 100.0%
Average number of contigs per scaffold 1.0
Average length of break (>25 Ns) between contigs in scaffold 0
Number of contigs 2968
Number of contigs in scaffolds 0
Number of contigs not in scaffolds 2968
Total size of contigs 185941456
Longest contig 1175772
Shortest contig 56
Number of contigs > 1K nt 2937 99.0%
Number of contigs > 10K nt 2346 79.0%
Number of contigs > 100K nt 486 16.4%
Number of contigs > 1M nt 4 0.1%
Number of contigs > 10M nt 0 0.0%
Mean contig size 62649
Median contig size 23092
N50 contig length 166627
L50 contig count 273
n90 contig length 23705
L90 contig count 1451
contig %A 31.52
contig %C 18.42
contig %G 18.45
contig %T 31.61
contig %N 0.00
contig %non-ACGTN 0.00
Number of contig non-ACGTN nt 0
--------------------------------------------------
|Results from dataset nematoda_odb10 |
--------------------------------------------------
|C:52.8%[S:46.6%,D:6.2%],F:2.3%,M:44.9%,n:3131 |
|1653 Complete BUSCOs (C) |
|1460 Complete and single-copy BUSCOs (S) |
|193 Complete and duplicated BUSCOs (D) |
|73 Fragmented BUSCOs (F) |
|1405 Missing BUSCOs (M) |
|3131 Total BUSCO groups searched |
--------------------------------------------------
---------------- Information for assembly 'all_p_ctg.fa' ----------------
Number of scaffolds 1544
Total size of scaffolds 166297003
Longest scaffold 1174918
Shortest scaffold 5015
Number of scaffolds > 1K nt 1544 100.0%
Number of scaffolds > 10K nt 1543 99.9%
Number of scaffolds > 100K nt 477 30.9%
Number of scaffolds > 1M nt 4 0.3%
Number of scaffolds > 10M nt 0 0.0%
Mean scaffold size 107705
Median scaffold size 57033
N50 scaffold length 198177
L50 scaffold count 224
n90 scaffold length 41813
L90 scaffold count 965
scaffold %A 31.54
scaffold %C 18.39
scaffold %G 18.42
scaffold %T 31.64
scaffold %N 0.00
scaffold %non-ACGTN 0.00
Number of scaffold non-ACGTN nt 0
Percentage of assembly in scaffolded contigs 0.0%
Percentage of assembly in unscaffolded contigs 100.0%
Average number of contigs per scaffold 1.0
Average length of break (>25 Ns) between contigs in scaffold 0
Number of contigs 1544
Number of contigs in scaffolds 0
Number of contigs not in scaffolds 1544
Total size of contigs 166297003
Longest contig 1174918
Shortest contig 5015
Number of contigs > 1K nt 1544 100.0%
Number of contigs > 10K nt 1543 99.9%
Number of contigs > 100K nt 477 30.9%
Number of contigs > 1M nt 4 0.3%
Number of contigs > 10M nt 0 0.0%
Mean contig size 107705
Median contig size 57033
N50 contig length 198177
L50 contig count 224
n90 contig length 41813
L90 contig count 965
contig %A 31.54
contig %C 18.39
contig %G 18.42
contig %T 31.64
contig %N 0.00
contig %non-ACGTN 0.00
Number of contig non-ACGTN nt 0
--------------------------------------------------
|Results from dataset nematoda_odb10 |
--------------------------------------------------
|C:52.2%[S:46.7%,D:5.5%],F:2.5%,M:45.3%,n:3131 |
|1634 Complete BUSCOs (C) |
|1461 Complete and single-copy BUSCOs (S) |
|173 Complete and duplicated BUSCOs (D) |
|77 Fragmented BUSCOs (F) |
|1420 Missing BUSCOs (M) |
|3131 Total BUSCO groups searched |
--------------------------------------------------
#/work/gif/remkv6/Baum/04_DovetailSCNGenome/01_CondoPorts/04_GapFilling
---------------- Information for assembly 'nematode_sp_19Jul2018_IbtP1.fasta' ----------------
Number of scaffolds 590
Total size of scaffolds 166433103
Longest scaffold 20440036
Shortest scaffold 536
Number of scaffolds > 1K nt 589 99.8%
Number of scaffolds > 10K nt 580 98.3%
Number of scaffolds > 100K nt 135 22.9%
Number of scaffolds > 1M nt 16 2.7%
Number of scaffolds > 10M nt 6 1.0%
Mean scaffold size 282090
Median scaffold size 44252
N50 scaffold length 10944860
L50 scaffold count 6
n90 scaffold length 87674
L90 scaffold count 161
scaffold %A 31.58
scaffold %C 18.39
scaffold %G 18.39
scaffold %T 31.56
scaffold %N 0.08
scaffold %non-ACGTN 0.00
Number of scaffold non-ACGTN nt 0
Percentage of assembly in scaffolded contigs 90.8%
Percentage of assembly in unscaffolded contigs 9.2%
Average number of contigs per scaffold 3.3
Average length of break (>25 Ns) between contigs in scaffold 100
Number of contigs 1951
Number of contigs in scaffolds 1577
Number of contigs not in scaffolds 374
Total size of contigs 166297003
Longest contig 1155511
Shortest contig 173
Number of contigs > 1K nt 1937 99.3%
Number of contigs > 10K nt 1896 97.2%
Number of contigs > 100K nt 449 23.0%
Number of contigs > 1M nt 3 0.2%
Number of contigs > 10M nt 0 0.0%
Mean contig size 85237
Median contig size 50218
N50 contig length 137872
L50 contig count 302
n90 contig length 36314
L90 contig count 1263
contig %A 31.60
contig %C 18.40
contig %G 18.41
contig %T 31.58
contig %N 0.00
contig %non-ACGTN 0.00
Number of contig non-ACGTN nt 0
--------------------------------------------------
|Results from dataset nematoda_odb10 |
--------------------------------------------------
|C:52.1%[S:48.1%,D:4.0%],F:2.2%,M:45.7%,n:3131 |
|1632 Complete BUSCOs (C) |
|1507 Complete and single-copy BUSCOs (S) |
|125 Complete and duplicated BUSCOs (D) |
|70 Fragmented BUSCOs (F) |
|1429 Missing BUSCOs (M) |
|3131 Total BUSCO groups searched |
--------------------------------------------------
#lost this file
~/common_scripts/new_Assemblathon.pl PacBio_scaffolder_results/scaffolds.fasta
Number of scaffolds 396
Total size of scaffolds 166863111
Longest scaffold 31384913
Shortest scaffold 536
Number of scaffolds > 1K nt 395 99.7%
Number of scaffolds > 10K nt 390 98.5%
Number of scaffolds > 100K nt 138 34.8%
Number of scaffolds > 1M nt 15 3.8%
Number of scaffolds > 10M nt 5 1.3%
Mean scaffold size 421371
Median scaffold size 64938
N50 scaffold length 11380747
L50 scaffold count 5
scaffold %A 31.50
scaffold %C 18.35
scaffold %G 18.34
scaffold %T 31.47
scaffold %N 0.34
scaffold %non-ACGTN 0.00
Number of scaffold non-ACGTN nt 0
Percentage of assembly in scaffolded contigs 95.6%
Percentage of assembly in unscaffolded contigs 4.4%
Average number of contigs per scaffold 4.8
Average length of break (>25 Ns) between contigs in scaffold 375
Number of contigs 1902
Number of contigs in scaffolds 1711
Number of contigs not in scaffolds 191
Total size of contigs 166297033
Longest contig 1155511
Shortest contig 173
Number of contigs > 1K nt 1890 99.4%
Number of contigs > 10K nt 1853 97.4%
Number of contigs > 100K nt 459 24.1%
Number of contigs > 1M nt 3 0.2%
Number of contigs > 10M nt 0 0.0%
Mean contig size 87433
Median contig size 52046
N50 contig length 143481
L50 contig count 298
contig %A 31.61
contig %C 18.41
contig %G 18.40
contig %T 31.58
contig %N 0.00
contig %non-ACGTN 0.00
Number of contig non-ACGTN nt 0
---------------- Information for assembly '/dev/fd/63' ----------------
Number of scaffolds 396
Total size of scaffolds 166141519
Longest scaffold 31274080
Shortest scaffold 536
Number of scaffolds > 1K nt 395 99.7%
Number of scaffolds > 10K nt 390 98.5%
Number of scaffolds > 100K nt 138 34.8%
Number of scaffolds > 1M nt 15 3.8%
Number of scaffolds > 10M nt 5 1.3%
Mean scaffold size 419549
Median scaffold size 64938
N50 scaffold length 11339714
L50 scaffold count 5
n90 scaffold length 148770
L90 scaffold count 96
scaffold %A 31.50
scaffold %C 18.35
scaffold %G 18.34
scaffold %T 31.47
scaffold %N 0.34
scaffold %non-ACGTN 0.00
Number of scaffold non-ACGTN nt 0
Percentage of assembly in scaffolded contigs 95.4%
Percentage of assembly in unscaffolded contigs 4.6%
Average number of contigs per scaffold 4.6
Average length of break (>25 Ns) between contigs in scaffold 387
Number of contigs 1838
Number of contigs in scaffolds 1643
Number of contigs not in scaffolds 195
Total size of contigs 165582321
Longest contig 1155511
Shortest contig 173
Number of contigs > 1K nt 1826 99.3%
Number of contigs > 10K nt 1792 97.5%
Number of contigs > 100K nt 453 24.6%
Number of contigs > 1M nt 4 0.2%
Number of contigs > 10M nt 0 0.0%
Mean contig size 90088
Median contig size 52203
N50 contig length 150283
L50 contig count 276
n90 contig length 37695
L90 contig count 1177
contig %A 31.61
contig %C 18.41
contig %G 18.40
contig %T 31.58
contig %N 0.00
contig %non-ACGTN 0.00
Number of contig non-ACGTN nt 0
--------------------------------------------------
--------------------------------------------------
|Results from dataset nematoda_odb10 |
--------------------------------------------------
|C:52.1%[S:48.4%,D:3.7%],F:2.2%,M:45.7%,n:3131 |
|1631 Complete BUSCOs (C) |
|1516 Complete and single-copy BUSCOs (S) |
|115 Complete and duplicated BUSCOs (D) |
|70 Fragmented BUSCOs (F) |
|1430 Missing BUSCOs (M) |
|3131 Total BUSCO groups searched |
--------------------------------------------------
#/work/gif/remkv6/Baum/04_DovetailSCNGenome/01_CondoPorts/04_GapFilling/07_Split1Pilon/01_misassemblyTest
---------------- Information for assembly 'PilonFixedGenome.fa' ----------------
Number of scaffolds 396
Total size of scaffolds 166326526
Longest scaffold 31310481
Shortest scaffold 536
Number of scaffolds > 1K nt 394 99.5%
Number of scaffolds > 10K nt 390 98.5%
Number of scaffolds > 100K nt 138 34.8%
Number of scaffolds > 1M nt 15 3.8%
Number of scaffolds > 10M nt 5 1.3%
Mean scaffold size 420016
Median scaffold size 64978
N50 scaffold length 11353933
L50 scaffold count 5
n90 scaffold length 149011
L90 scaffold count 96
scaffold %A 31.57
scaffold %C 18.27
scaffold %G 18.28
scaffold %T 31.54
scaffold %N 0.33
scaffold %non-ACGTN 0.00
Number of scaffold non-ACGTN nt 0
Percentage of assembly in scaffolded contigs 94.6%
Percentage of assembly in unscaffolded contigs 5.4%
Average number of contigs per scaffold 3.7
Average length of break (>25 Ns) between contigs in scaffold 502
Number of contigs 1477
Number of contigs in scaffolds 1266
Number of contigs not in scaffolds 211
Total size of contigs 165783581
Longest contig 1418461
Shortest contig 106
Number of contigs > 1K nt 1472 99.7%
Number of contigs > 10K nt 1446 97.9%
Number of contigs > 100K nt 441 29.9%
Number of contigs > 1M nt 9 0.6%
Number of contigs > 10M nt 0 0.0%
Mean contig size 112243
Median contig size 54845
N50 contig length 234113
L50 contig count 193
n90 contig length 43520
L90 contig count 876
contig %A 31.68
contig %C 18.33
contig %G 18.34
contig %T 31.65
contig %N 0.00
contig %non-ACGTN 0.00
Number of contig non-ACGTN nt 0
--------------------------------------------------
|Results from dataset nematoda_odb10 |
--------------------------------------------------
|C:56.0%[S:51.9%,D:4.1%],F:2.1%,M:41.9%,n:3131 |
|1754 Complete BUSCOs (C) |
|1626 Complete and single-copy BUSCOs (S) |
|128 Complete and duplicated BUSCOs (D) |
|66 Fragmented BUSCOs (F) |
|1311 Missing BUSCOs (M) |
|3131 Total BUSCO groups searched |
--------------------------------------------------
#/work/gif/remkv6/Baum/04_DovetailSCNGenome/01_CondoPorts/04_GapFilling/12_Pilon2ndRun
---------------- Information for assembly 'MisAssFixed.Pilon.FINAL.fasta' ----------------
Number of scaffolds 9
Total size of scaffolds 158541936
Longest scaffold 24162073
Shortest scaffold 10911090
Number of scaffolds > 1K nt 9 100.0%
Number of scaffolds > 10K nt 9 100.0%
Number of scaffolds > 100K nt 9 100.0%
Number of scaffolds > 1M nt 9 100.0%
Number of scaffolds > 10M nt 9 100.0%
Mean scaffold size 17615771
Median scaffold size 16842261
N50 scaffold length 17946823
L50 scaffold count 4
n90 scaffold length 12293705
L90 scaffold count 8
scaffold %A 31.32
scaffold %C 18.10
scaffold %G 18.13
scaffold %T 31.31
scaffold %N 1.13
scaffold %non-ACGTN 0.00
Number of scaffold non-ACGTN nt 0
Percentage of assembly in scaffolded contigs 100.0%
Percentage of assembly in unscaffolded contigs 0.0%
Average number of contigs per scaffold 264.0
Average length of break (>25 Ns) between contigs in scaffold 756
Number of contigs 2376
Number of contigs in scaffolds 2376
Number of contigs not in scaffolds 0
Total size of contigs 156744176
Longest contig 811002
Shortest contig 221
Number of contigs > 1K nt 2344 98.7%
Number of contigs > 10K nt 2140 90.1%
Number of contigs > 100K nt 462 19.4%
Number of contigs > 1M nt 0 0.0%
Number of contigs > 10M nt 0 0.0%
Mean contig size 65970
Median contig size 38009
N50 contig length 116317
L50 contig count 379
n90 contig length 27869
L90 contig count 1452
contig %A 31.68
contig %C 18.31
contig %G 18.34
contig %T 31.67
contig %N 0.00
contig %non-ACGTN 0.00
Number of contig non-ACGTN nt 0
--------------------------------------------------
|Results from dataset nematoda_odb10 |
--------------------------------------------------
|C:54.5%[S:51.3%,D:3.2%],F:2.5%,M:43.0%,n:3131 |
|1706 Complete BUSCOs (C) |
|1606 Complete and single-copy BUSCOs (S) |
|100 Complete and duplicated BUSCOs (D) |
|78 Fragmented BUSCOs (F) |
|1347 Missing BUSCOs (M) |
|3131 Total BUSCO groups searched |
--------------------------------------------------
cd
#/work/gif/remkv6/Baum/04_DovetailSCNGenome/01_CondoPorts/04_GapFilling/12_Pilon2ndRun/Assembly
---------------- Information for assembly 'WholeGenome.fa' ----------------
Number of scaffolds 9
Total size of scaffolds 158343599
Longest scaffold 24096054
Shortest scaffold 10903567
Number of scaffolds > 1K nt 9 100.0%
Number of scaffolds > 10K nt 9 100.0%
Number of scaffolds > 100K nt 9 100.0%
Number of scaffolds > 1M nt 9 100.0%
Number of scaffolds > 10M nt 9 100.0%
Mean scaffold size 17593733
Median scaffold size 16822016
N50 scaffold length 17936192
L50 scaffold count 4
n90 scaffold length 12280959
L90 scaffold count 8
scaffold %A 31.33
scaffold %C 18.11
scaffold %G 18.14
scaffold %T 31.32
scaffold %N 1.10
scaffold %non-ACGTN 0.00
Number of scaffold non-ACGTN nt 0
Percentage of assembly in scaffolded contigs 100.0%
Percentage of assembly in unscaffolded contigs 0.0%
Average number of contigs per scaffold 247.8
Average length of break (>25 Ns) between contigs in scaffold 782
Number of contigs 2230
Number of contigs in scaffolds 2230
Number of contigs not in scaffolds 0
Total size of contigs 156598730
Longest contig 835801
Shortest contig 221
Number of contigs > 1K nt 2210 99.1%
Number of contigs > 10K nt 2018 90.5%
Number of contigs > 100K nt 472 21.2%
Number of contigs > 1M nt 0 0.0%
Number of contigs > 10M nt 0 0.0%
Mean contig size 70224
Median contig size 39153
N50 contig length 125056
L50 contig count 343
n90 contig length 29058
L90 contig count 1340
contig %A 31.68
contig %C 18.31
contig %G 18.34
contig %T 31.67
contig %N 0.00
contig %non-ACGTN 0.00
Number of contig non-ACGTN nt 0
--------------------------------------------------
|Results from dataset nematoda_odb10 |
--------------------------------------------------
|C:55.3%[S:52.1%,D:3.2%],F:2.3%,M:42.4%,n:3131 |
|1733 Complete BUSCOs (C) |
|1632 Complete and single-copy BUSCOs (S) |
|101 Complete and duplicated BUSCOs (D) |
|73 Fragmented BUSCOs (F) |
|1325 Missing BUSCOs (M) |
|3131 Total BUSCO groups searched |
--------------------------------------------------
#/work/gif/remkv6/Baum/04_DovetailSCNGenome/01_CondoPorts/04_GapFilling/13_AlignCCSReads/13_Round11Pilon
---------------- Information for assembly 'Genome40.fasta' ----------------
Number of scaffolds 9
Total size of scaffolds 158061466
Longest scaffold 24020318
Shortest scaffold 10891489
Number of scaffolds > 1K nt 9 100.0%
Number of scaffolds > 10K nt 9 100.0%
Number of scaffolds > 100K nt 9 100.0%
Number of scaffolds > 1M nt 9 100.0%
Number of scaffolds > 10M nt 9 100.0%
Mean scaffold size 17562385
Median scaffold size 16800322
N50 scaffold length 17911831
L50 scaffold count 4
n90 scaffold length 12254402
L90 scaffold count 8
scaffold %A 31.34
scaffold %C 18.12
scaffold %G 18.15
scaffold %T 31.33
scaffold %N 1.07
scaffold %non-ACGTN 0.00
Number of scaffold non-ACGTN nt 0
Percentage of assembly in scaffolded contigs 100.0%
Percentage of assembly in unscaffolded contigs 0.0%
Average number of contigs per scaffold 238.6
Average length of break (>25 Ns) between contigs in scaffold 791
Number of contigs 2147
Number of contigs in scaffolds 2147
Number of contigs not in scaffolds 0
Total size of contigs 156363906
Longest contig 834409
Shortest contig 221
Number of contigs > 1K nt 2129 99.2%
Number of contigs > 10K nt 1944 90.5%
Number of contigs > 100K nt 480 22.4%
Number of contigs > 1M nt 0 0.0%
Number of contigs > 10M nt 0 0.0%
Mean contig size 72829
Median contig size 40242
N50 contig length 132490
L50 contig count 326
n90 contig length 30213
L90 contig count 1275
contig %A 31.68
contig %C 18.31
contig %G 18.34
contig %T 31.67
contig %N 0.00
contig %non-ACGTN 0.00
Number of contig non-ACGTN nt 0
--------------------------------------------------
|Results from dataset nematoda_odb10 |
--------------------------------------------------
|C:54.9%[S:51.7%,D:3.2%],F:2.3%,M:42.8%,n:3131 |
|1717 Complete BUSCOs (C) |
|1618 Complete and single-copy BUSCOs (S) |
|99 Complete and duplicated BUSCOs (D) |
|73 Fragmented BUSCOs (F) |
|1341 Missing BUSCOs (M) |
|3131 Total BUSCO groups searched |
--------------------------------------------------
---------------- Information for assembly 'Genome40.Pilon.fasta' ----------------
Number of scaffolds 9
Total size of scaffolds 157982452
Longest scaffold 23986085
Shortest scaffold 10884008
Number of scaffolds > 1K nt 9 100.0%
Number of scaffolds > 10K nt 9 100.0%
Number of scaffolds > 100K nt 9 100.0%
Number of scaffolds > 1M nt 9 100.0%
Number of scaffolds > 10M nt 9 100.0%
Mean scaffold size 17553606
Median scaffold size 16794675
N50 scaffold length 17908190
L50 scaffold count 4
n90 scaffold length 12250898
L90 scaffold count 8
scaffold %A 31.34
scaffold %C 18.12
scaffold %G 18.15
scaffold %T 31.33
scaffold %N 1.06
scaffold %non-ACGTN 0.00
Number of scaffold non-ACGTN nt 0
Percentage of assembly in scaffolded contigs 100.0%
Percentage of assembly in unscaffolded contigs 0.0%
Average number of contigs per scaffold 234.3
Average length of break (>25 Ns) between contigs in scaffold 797
Number of contigs 2109
Number of contigs in scaffolds 2109
Number of contigs not in scaffolds 0
Total size of contigs 156301043
Longest contig 834407
Shortest contig 221
Number of contigs > 1K nt 2094 99.3%
Number of contigs > 10K nt 1916 90.8%
Number of contigs > 100K nt 483 22.9%
Number of contigs > 1M nt 0 0.0%
Number of contigs > 10M nt 0 0.0%
Mean contig size 74111
Median contig size 41011
N50 contig length 140610
L50 contig count 320
n90 contig length 30618
L90 contig count 1248
contig %A 31.68
contig %C 18.31
contig %G 18.34
contig %T 31.66
contig %N 0.00
contig %non-ACGTN 0.00
Number of contig non-ACGTN nt 0
--------------------------------------------------
|Results from dataset nematoda_odb10 |
--------------------------------------------------
|C:55.6%[S:52.5%,D:3.1%],F:2.3%,M:42.1%,n:3131 |
|1740 Complete BUSCOs (C) |
|1644 Complete and single-copy BUSCOs (S) |
|96 Complete and duplicated BUSCOs (D) |
|72 Fragmented BUSCOs (F) |
|1319 Missing BUSCOs (M) |
|3131 Total BUSCO groups searched |
--------------------------------------------------