how to improve assembly contiguity for repeat genome

[wingwingWY]

Hi, I assembled a repetitive plant genome with promethION data by CANU 1.8. The genome size is about 1G and the input reads coverage is 90X . I got a 1.04G result with N50 118kb. How to improve the assembly? My command is :

canu -nanopore-raw ./data/*.gz  \
        -d ./output_remote -p SM  \
        genomeSize=1G \
        useGrid=remote   \
        overlapper=mhap utgReAlign=true \
        minReadLength=5000 

Should I remove "overlapper=mhap utgReAlign=true" and add " correctedErrorRate=0.15 corMhapSensivity=normal corOutCoverage=80 corMaxEvidenceErate=0.15 " to my command?

This is the report file:

[CORRECTION/READS]
--
-- In sequence store './SM.seqStore':
--   Found 8054538 reads.
--   Found 93899656611 bases (93.89 times coverage).
--
--   Read length histogram (one '*' equals 66588.28 reads):
--     5000   9999 4661180 **********************************************************************
--    10000  14999 1911018 ****************************
--    15000  19999 722516 **********
--    20000  24999 313009 ****
--    25000  29999 156161 **
--    30000  34999  89069 *
--    35000  39999  56605
--    40000  44999  38388
--    45000  49999  27637
--    50000  54999  19921
--    55000  59999  14887
--    60000  64999  11198
--    65000  69999   8490
--    70000  74999   6053
--    75000  79999   4607
--    80000  84999   3573
--    85000  89999   2597
--    90000  94999   1890
--    95000  99999   1390
--   100000 104999    976
--   105000 109999    773
--   110000 114999    563
--   115000 119999    395
--   120000 124999    286
--   125000 129999    234
--   130000 134999    161
--   135000 139999    127
--   140000 144999    104
--   145000 149999     81
--   150000 154999     58
--   155000 159999     46
--   160000 164999     33
--   165000 169999     45
--   170000 174999     25
--   175000 179999     35
--   180000 184999     27
--   185000 189999     25
--   190000 194999     18
--   195000 199999     15
--   200000 204999     12
--   205000 209999     13
--   210000 214999     14
--   215000 219999     14
--   220000 224999      5
--   225000 229999      8
--   230000 234999     12
--   235000 239999     11
--   240000 244999      7
--   245000 249999      5
--   250000 254999      6
--   255000 259999     14
--   260000 264999     11
--   265000 269999     16
--   270000 274999      9
--   275000 279999      6
--   280000 284999      5
--   285000 289999      4
--   290000 294999      4
--   295000 299999      8
--   300000 304999      5
--   305000 309999      4
--   310000 314999      8
--   315000 319999      4
--   320000 324999      2
--   325000 329999      2
--   330000 334999      7
--   335000 339999      2
--   340000 344999      4
--   345000 349999      4
--   350000 354999      1
--   355000 359999      1
--   360000 364999      6
--   365000 369999      2
--   370000 374999      3
--   375000 379999      5
--   380000 384999      4
--   385000 389999      0
--   390000 394999      2
--   395000 399999      2
--   400000 404999      3
--   405000 409999      3
--   410000 414999      1
--   415000 419999      0
--   420000 424999      6
--   425000 429999      1
--   430000 434999      3
--   435000 439999      2
--   440000 444999      2
--   445000 449999      3
--   450000 454999      3
--   455000 459999      0
--   460000 464999      2
--   465000 469999      1
--   470000 474999      2
--   475000 479999      1
--   480000 484999      2
--   485000 489999      1
--   490000 494999      1
--   495000 499999      3
--   500000 504999      1
--   505000 509999      0
--   510000 514999      0
--   515000 519999      1
--   520000 524999      1
--   525000 529999      0
--   530000 534999      1
--   535000 539999      3
--   540000 544999      0
--   545000 549999      1
--   550000 554999      1
--   555000 559999      0
--   560000 564999      0
--   565000 569999      1
--   570000 574999      0
--   575000 579999      1
--   580000 584999      2
--   585000 589999      1
--   590000 594999      1
--   595000 599999      0
--   600000 604999      0
--   605000 609999      0
--   610000 614999      1
--   615000 619999      2
--   620000 624999      0
--   625000 629999      0
--   630000 634999      2
--   635000 639999      1
--   640000 644999      0
--   645000 649999      0
--   650000 654999      1
--   655000 659999      0
--   660000 664999      1
--   665000 669999      0
--   670000 674999      0
--   675000 679999      0
--   680000 684999      0
--   685000 689999      0
--   690000 694999      0
--   695000 699999      1
--   700000 704999      0
--   705000 709999      0
--   710000 714999      1
--   715000 719999      0
--   720000 724999      0
--   725000 729999      0
--   730000 734999      0
--   735000 739999      0
--   740000 744999      0
--   745000 749999      0
--   750000 754999      0
--   755000 759999      1
--   760000 764999      0
--   765000 769999      0
--   770000 774999      2
--   775000 779999      1
--   780000 784999      0
--   785000 789999      0
--   790000 794999      0
--   795000 799999      0
--   800000 804999      0
--   805000 809999      0
--   810000 814999      0
--   815000 819999      0
--   820000 824999      0
--   825000 829999      0
--   830000 834999      0
--   835000 839999      0
--   840000 844999      0
--   845000 849999      0
--   850000 854999      1

[CORRECTION/MERS]
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2  46382624 ***********                                                            0.0221 0.0010
--       3-     4 123348691 *******************************                                        0.0496 0.0028
--       5-     7 213362661 ******************************************************                 0.1140 0.0094
--       8-    11 268477901 *********************************************************************  0.2158 0.0253
--      12-    16 272175150 ********************************************************************** 0.3386 0.0541
--      17-    22 241836872 **************************************************************         0.4613 0.0951
--      23-    29 199404528 ***************************************************                    0.5702 0.1447
--      30-    37 158064359 ****************************************                               0.6603 0.1989
--      38-    46 123098618 *******************************                                        0.7321 0.2541
--      47-    56  95249813 ************************                                               0.7884 0.3079
--      57-    67  73517910 ******************                                                     0.8321 0.3591
--      68-    79  56765405 **************                                                         0.8660 0.4067
--      80-    92  43973405 ***********                                                            0.8922 0.4504
--      93-   106  34275984 ********                                                               0.9126 0.4900
--     107-   121  26914656 ******                                                                 0.9286 0.5258
--     122-   137  21308894 *****                                                                  0.9411 0.5581
--     138-   154  17014947 ****                                                                   0.9511 0.5871
--     155-   172  13686801 ***                                                                    0.9590 0.6133
--     173-   191  11103878 **                                                                     0.9654 0.6369
--     192-   211   9070688 **                                                                     0.9706 0.6582
--     212-   232   7460063 *                                                                      0.9749 0.6775
--     233-   254   6176728 *                                                                      0.9784 0.6950
--     255-   277   5149363 *                                                                      0.9813 0.7110
--     278-   301   4322595 *                                                                      0.9837 0.7255
--     302-   326   3647677                                                                        0.9858 0.7387
--     327-   352   3100168                                                                        0.9875 0.7509
--     353-   379   2646636                                                                        0.9890 0.7620
--     380-   407   2268322                                                                        0.9902 0.7723
--     408-   436   1959031                                                                        0.9913 0.7818
--     437-   466   1694806                                                                        0.9922 0.7905
--     467-   497   1473446                                                                        0.9930 0.7987
--     498-   529   1286264                                                                        0.9937 0.8062
--     530-   562   1126456                                                                        0.9943 0.8132
--     563-   596    989321                                                                        0.9949 0.8198
--     597-   631    871843                                                                        0.9953 0.8258
--     632-   667    771976                                                                        0.9957 0.8315
--     668-   704    683042                                                                        0.9961 0.8369
--     705-   742    609075                                                                        0.9964 0.8419
--     743-   781    543521                                                                        0.9967 0.8465
--     782-   821    487520                                                                        0.9970 0.8509
--
--           0 (max occurrences)
-- 93747658429 (total mers, non-unique)
--  2102196813 (distinct mers, non-unique)
--           0 (unique mers)

[CORRECTION/LAYOUT]
--                             original      original
--                            raw reads     raw reads
--   category                w/overlaps  w/o/overlaps
--   -------------------- ------------- -------------
--   Number of Reads            6733864       1320674
--   Number of Bases        80848084858    4371783844
--   Coverage                    80.848         4.372
--   Median                        9324             0
--   Mean                         12006          3310
--   N50                          12867          9819
--   Minimum                       5000             0
--   Maximum                     853997        331122
--
--                                        --------corrected---------  ----------rescued----------
--                             evidence                     expected                     expected
--   category                     reads            raw     corrected            raw     corrected
--   -------------------- -------------  ------------- -------------  ------------- -------------
--   Number of Reads            6931480        2791888       2791888           4996          4996
--   Number of Bases        82907295251    45929317749   40000003829       32790505      32188591
--   Coverage                    82.907         45.929        40.000          0.033         0.032
--   Median                        9305          12782         11638           6485          6440
--   Mean                         11960          16450         14327           6563          6442
--   N50                          12798          17130         14372           6658          6588
--   Minimum                       5000           7899          7898           5002          5001
--   Maximum                     853997         853997        735526          36199          7898
--
--                        --------uncorrected--------
--                                           expected
--   category                       raw     corrected
--   -------------------- ------------- -------------
--   Number of Reads            5257654       5257654
--   Number of Bases        39257760448   12653341317
--   Coverage                    39.258        12.653
--   Median                        6969           250
--   Mean                          7466          2406
--   N50                           8687          6236
--   Minimum                          0             0
--   Maximum                     771637        771624
--
--   Maximum Memory          4290457316

[TRIMMING/READS]
--
-- In sequence store './SM.seqStore':
--   Found 2794627 reads.
--   Found 39334078360 bases (39.33 times coverage).
--
--   Read length histogram (one '*' equals 15233.67 reads):
--        0   4999   8207
--     5000   9999 953372 **************************************************************
--    10000  14999 1066357 **********************************************************************
--    15000  19999 394017 *************************
--    20000  24999 165798 **********
--    25000  29999  80000 *****
--    30000  34999  44304 **
--    35000  39999  26947 *
--    40000  44999  17419 *
--    45000  49999  11756
--    50000  54999   8171
--    55000  59999   5467
--    60000  64999   3950
--    65000  69999   2663
--    70000  74999   1729
--    75000  79999   1297
--    80000  84999    898
--    85000  89999    600
--    90000  94999    427
--    95000  99999    284
--   100000 104999    176
--   105000 109999    135
--   110000 114999     84
--   115000 119999     84
--   120000 124999     57
--   125000 129999     41
--   130000 134999     28
--   135000 139999     19
--   140000 144999     24
--   145000 149999     26
--   150000 154999     20
--   155000 159999     12
--   160000 164999     12
--   165000 169999     15
--   170000 174999     13
--   175000 179999     11
--   180000 184999      8
--   185000 189999      7
--   190000 194999      5
--   195000 199999     10
--   200000 204999      9
--   205000 209999      4
--   210000 214999      8
--   215000 219999      3
--   220000 224999      6
--   225000 229999      5
--   230000 234999      6
--   235000 239999      4
--   240000 244999      3
--   245000 249999      2
--   250000 254999      2
--   255000 259999     11
--   260000 264999      7
--   265000 269999      7
--   270000 274999      1
--   275000 279999      6
--   280000 284999      2
--   285000 289999      4
--   290000 294999      3
--   295000 299999      2
--   300000 304999      5
--   305000 309999      1
--   310000 314999      6
--   315000 319999      2
--   320000 324999      0
--   325000 329999      5
--   330000 334999      2
--   335000 339999      2
--   340000 344999      3
--   345000 349999      4
--   350000 354999      3
--   355000 359999      1
--   360000 364999      1
--   365000 369999      3
--   370000 374999      2
--   375000 379999      2
--   380000 384999      1
--   385000 389999      0
--   390000 394999      1
--   395000 399999      2
--   400000 404999      1
--   405000 409999      2
--   410000 414999      1
--   415000 419999      3
--   420000 424999      1
--   425000 429999      0
--   430000 434999      2
--   435000 439999      1
--   440000 444999      2
--   445000 449999      0
--   450000 454999      0
--   455000 459999      0
--   460000 464999      2
--   465000 469999      1
--   470000 474999      1
--   475000 479999      0
--   480000 484999      2
--   485000 489999      1
--   490000 494999      0
--   495000 499999      0
--   500000 504999      0
--   505000 509999      0
--   510000 514999      1
--   515000 519999      1
--   520000 524999      0
--   525000 529999      0
--   530000 534999      1
--   535000 539999      0
--   540000 544999      0
--   545000 549999      1
--   550000 554999      0
--   555000 559999      1
--   560000 564999      0
--   565000 569999      2
--   570000 574999      1
--   575000 579999      0
--   580000 584999      1
--   585000 589999      2
--   590000 594999      0
--   595000 599999      0
--   600000 604999      1
--   605000 609999      0
--   610000 614999      0
--   615000 619999      0
--   620000 624999      1
--   625000 629999      0
--   630000 634999      1
--   635000 639999      1
--   640000 644999      0
--   645000 649999      0
--   650000 654999      0
--   655000 659999      0
--   660000 664999      0
--   665000 669999      1

[TRIMMING/MERS]
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2 241736887 ***************************************************************        0.2024 0.0124
--       3-     4 266762681 ********************************************************************** 0.3345 0.0246
--       5-     7 185368786 ************************************************                       0.4919 0.0460
--       8-    11 114686668 ******************************                                         0.6121 0.0712
--      12-    16  72041216 ******************                                                     0.6924 0.0966
--      17-    22  48327993 ************                                                           0.7456 0.1207
--      23-    29  35637595 *********                                                              0.7828 0.1438
--      30-    37  29946873 *******                                                                0.8110 0.1671
--      38-    46  29981058 *******                                                                0.8355 0.1928
--      47-    56  34380277 *********                                                              0.8605 0.2260
--      57-    67  34014725 ********                                                               0.8894 0.2725
--      68-    79  22681471 *****                                                                  0.9171 0.3258
--      80-    92  13736769 ***                                                                    0.9351 0.3666
--      93-   106  10856639 **                                                                     0.9462 0.3961
--     107-   121   9492717 **                                                                     0.9551 0.4237
--     122-   137   7578232 *                                                                      0.9630 0.4513
--     138-   154   5707111 *                                                                      0.9692 0.4760
--     155-   172   4593290 *                                                                      0.9739 0.4971
--     173-   191   3771896                                                                        0.9777 0.5163
--     192-   211   3060372                                                                        0.9808 0.5337
--     212-   232   2520360                                                                        0.9833 0.5494
--     233-   254   2098073                                                                        0.9854 0.5637
--     255-   277   1761557                                                                        0.9871 0.5767
--     278-   301   1488467                                                                        0.9886 0.5887
--     302-   326   1268411                                                                        0.9898 0.5997
--     327-   352   1088529                                                                        0.9909 0.6098
--     353-   379    941628                                                                        0.9918 0.6193
--     380-   407    817185                                                                        0.9926 0.6281
--     408-   436    712706                                                                        0.9932 0.6363
--     437-   466    625187                                                                        0.9938 0.6440
--     467-   497    551955                                                                        0.9944 0.6513
--     498-   529    488879                                                                        0.9948 0.6581
--     530-   562    433774                                                                        0.9952 0.6645
--     563-   596    388613                                                                        0.9956 0.6706
--     597-   631    346881                                                                        0.9959 0.6763
--     632-   667    313007                                                                        0.9962 0.6818
--     668-   704    283737                                                                        0.9965 0.6870
--     705-   742    255493                                                                        0.9967 0.6920
--     743-   781    232893                                                                        0.9969 0.6967
--     782-   821    211915                                                                        0.9971 0.7013
--
--           0 (max occurrences)
-- 38904906749 (total mers, non-unique)
--  1194444260 (distinct mers, non-unique)
--           0 (unique mers)

[TRIMMING/TRIMMING]
--  PARAMETERS:
--  ----------
--     5000    (reads trimmed below this many bases are deleted)
--   0.1200    (use overlaps at or below this fraction error)
--        1    (break region if overlap is less than this long, for 'largest covered' algorithm)
--        1    (break region if overlap coverage is less than this many read, for 'largest covered' algorithm)
--
--  INPUT READS:
--  -----------
--  8054538 reads  39334078360 bases (reads processed)
--       0 reads            0 bases (reads not processed, previously deleted)
--       0 reads            0 bases (reads not processed, in a library where trimming isn't allowed)
--
--  OUTPUT READS:
--  ------------
--  2776813 reads  39028735912 bases (trimmed reads output)
--       0 reads            0 bases (reads with no change, kept as is)
--  5265269 reads     52237679 bases (reads with no overlaps, deleted)
--   12456 reads     73114089 bases (reads with short trimmed length, deleted)
--
--  TRIMMING DETAILS:
--  ----------------
--  492696 reads     78199262 bases (bases trimmed from the 5' end of a read)
--  2776813 reads    101791418 bases (bases trimmed from the 3' end of a read)

[TRIMMING/SPLITTING]
--  PARAMETERS:
--  ----------
--     5000    (reads trimmed below this many bases are deleted)
--   0.1200    (use overlaps at or below this fraction error)
--  INPUT READS:
--  -----------
--  2776813 reads  39208726592 bases (reads processed)
--  5277725 reads    125351768 bases (reads not processed, previously deleted)
--       0 reads            0 bases (reads not processed, in a library where trimming isn't allowed)
--
--  PROCESSED:
--  --------
--       0 reads            0 bases (no overlaps)
--      24 reads       388237 bases (no coverage after adjusting for trimming done already)
--       0 reads            0 bases (processed for chimera)
--       0 reads            0 bases (processed for spur)
--  2776789 reads  39208338355 bases (processed for subreads)
--
--  READS WITH SIGNALS:
--  ------------------
--       0 reads            0 signals (number of 5' spur signal)
--       0 reads            0 signals (number of 3' spur signal)
--       0 reads            0 signals (number of chimera signal)
--    5983 reads         6042 signals (number of subread signal)
--
--  SIGNALS:
--  -------
--       0 reads            0 bases (size of 5' spur signal)
--       0 reads            0 bases (size of 3' spur signal)
--       0 reads            0 bases (size of chimera signal)
--    6042 reads      2246510 bases (size of subread signal)
--
--  TRIMMING:
--  --------
--     894 reads      7743162 bases (trimmed from the 5' end of the read)
--    5089 reads     43740146 bases (trimmed from the 3' end of the read)

[UNITIGGING/READS]
--
-- In sequence store './SM.seqStore':
--   Found 2776305 reads.
--   Found 38974957625 bases (38.97 times coverage).
--
--   Read length histogram (one '*' equals 15126.41 reads):
--     5000   9999 961985 ***************************************************************
--    10000  14999 1058849 **********************************************************************
--    15000  19999 389598 *************************
--    20000  24999 163134 **********
--    25000  29999  78508 *****
--    30000  34999  43498 **
--    35000  39999  26431 *
--    40000  44999  16996 *
--    45000  49999  11513
--    50000  54999   7996
--    55000  59999   5413
--    60000  64999   3816
--    65000  69999   2584
--    70000  74999   1676
--    75000  79999   1253
--    80000  84999    858
--    85000  89999    576
--    90000  94999    416
--    95000  99999    274
--   100000 104999    168
--   105000 109999    131
--   110000 114999     81
--   115000 119999     76
--   120000 124999     56
--   125000 129999     38
--   130000 134999     28
--   135000 139999     20
--   140000 144999     23
--   145000 149999     24
--   150000 154999     19
--   155000 159999     12
--   160000 164999     13
--   165000 169999     13
--   170000 174999     12
--   175000 179999     11
--   180000 184999      8
--   185000 189999      7
--   190000 194999      5
--   195000 199999     10
--   200000 204999      9
--   205000 209999      3
--   210000 214999      8
--   215000 219999      3
--   220000 224999      6
--   225000 229999      5
--   230000 234999      6
--   235000 239999      4
--   240000 244999      3
--   245000 249999      2
--   250000 254999      2
--   255000 259999     11
--   260000 264999      7
--   265000 269999      7
--   270000 274999      1
--   275000 279999      6
--   280000 284999      2
--   285000 289999      4
--   290000 294999      3
--   295000 299999      2
--   300000 304999      5
--   305000 309999      1
--   310000 314999      6
--   315000 319999      3
--   320000 324999      0
--   325000 329999      5
--   330000 334999      3
--   335000 339999      2
--   340000 344999      2
--   345000 349999      4
--   350000 354999      3
--   355000 359999      1
--   360000 364999      1
--   365000 369999      3
--   370000 374999      2
--   375000 379999      2
--   380000 384999      1
--   385000 389999      0
--   390000 394999      1
--   395000 399999      2
--   400000 404999      1
--   405000 409999      2
--   410000 414999      1
--   415000 419999      2
--   420000 424999      1
--   425000 429999      0
--   430000 434999      2
--   435000 439999      1
--   440000 444999      2
--   445000 449999      0
--   450000 454999      0
--   455000 459999      0
--   460000 464999      2
--   465000 469999      1
--   470000 474999      1
--   475000 479999      0
--   480000 484999      2
--   485000 489999      1
--   490000 494999      0
--   495000 499999      0
--   500000 504999      0
--   505000 509999      0
--   510000 514999      1
--   515000 519999      1
--   520000 524999      0
--   525000 529999      0
--   530000 534999      1
--   535000 539999      0
--   540000 544999      0
--   545000 549999      1
--   550000 554999      0
--   555000 559999      1
--   560000 564999      0
--   565000 569999      3
--   570000 574999      1
--   575000 579999      0
--   580000 584999      0
--   585000 589999      2
--   590000 594999      0
--   595000 599999      0
--   600000 604999      1
--   605000 609999      0
--   610000 614999      0
--   615000 619999      0
--   620000 624999      1
--   625000 629999      0
--   630000 634999      1
--   635000 639999      1
--   640000 644999      0
--   645000 649999      0
--   650000 654999      0
--   655000 659999      0
--   660000 664999      0
--   665000 669999      1

[UNITIGGING/MERS]
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2 240071250 ***************************************************************        0.2032 0.0125
--       3-     4 263586337 ********************************************************************** 0.3352 0.0246
--       5-     7 182632968 ************************************************                       0.4922 0.0459
--       8-    11 112922494 *****************************                                          0.6118 0.0710
--      12-    16  70980443 ******************                                                     0.6917 0.0962
--      17-    22  47693657 ************                                                           0.7447 0.1202
--      23-    29  35264443 *********                                                              0.7818 0.1432
--      30-    37  29762570 *******                                                                0.8101 0.1664
--      38-    46  29964579 *******                                                                0.8346 0.1923
--      47-    56  34447874 *********                                                              0.8600 0.2258
--      57-    67  33867740 ********                                                               0.8892 0.2728
--      68-    79  22380601 *****                                                                  0.9170 0.3263
--      80-    92  13576058 ***                                                                    0.9350 0.3669
--      93-   106  10790233 **                                                                     0.9461 0.3964
--     107-   121   9432568 **                                                                     0.9551 0.4241
--     122-   137   7501384 *                                                                      0.9629 0.4517
--     138-   154   5648081 *                                                                      0.9692 0.4765
--     155-   172   4551435 *                                                                      0.9738 0.4975
--     173-   191   3735578                                                                        0.9776 0.5167
--     192-   211   3029717                                                                        0.9808 0.5341
--     212-   232   2494511                                                                        0.9833 0.5498
--     233-   254   2076038                                                                        0.9854 0.5640
--     255-   277   1743414                                                                        0.9871 0.5771
--     278-   301   1473883                                                                        0.9886 0.5890
--     302-   326   1254782                                                                        0.9898 0.6000
--     327-   352   1077119                                                                        0.9909 0.6102
--     353-   379    931483                                                                        0.9918 0.6196
--     380-   407    808539                                                                        0.9926 0.6284
--     408-   436    705280                                                                        0.9932 0.6366
--     437-   466    618707                                                                        0.9938 0.6443
--     467-   497    546365                                                                        0.9944 0.6515
--     498-   529    483338                                                                        0.9948 0.6583
--     530-   562    429159                                                                        0.9952 0.6647
--     563-   596    384358                                                                        0.9956 0.6708
--     597-   631    343270                                                                        0.9959 0.6766
--     632-   667    309751                                                                        0.9962 0.6820
--     668-   704    280510                                                                        0.9965 0.6872
--     705-   742    252862                                                                        0.9967 0.6922
--     743-   781    230833                                                                        0.9969 0.6969
--     782-   821    209389                                                                        0.9971 0.7015
--
--           0 (max occurrences)
-- 38545332250 (total mers, non-unique)
--  1181711145 (distinct mers, non-unique)
--           0 (unique mers)

[UNITIGGING/OVERLAPS]
--   category            reads     %          read length        feature size or coverage  analysis
--   ----------------  -------  -------  ----------------------  ------------------------  --------------------
--   middle-missing       9063    0.33    19051.11 +- 21921.71      2102.52 +- 7186.63    (bad trimming)
--   middle-hump          3015    0.11    28347.99 +- 34716.30     14028.44 +- 29645.06   (bad trimming)
--   no-5-prime          24773    0.89    15336.51 +- 12809.04      2271.02 +- 6941.58    (bad trimming)
--   no-3-prime          25673    0.92    14988.35 +- 11558.35      2246.12 +- 3863.03    (bad trimming)
--
--   low-coverage        90650    3.27    10458.42 +- 3458.96          5.84 +- 2.97       (easy to assemble, potential for lower quality consensus)
--   unique            1028428   37.04    12265.83 +- 5205.61         40.86 +- 11.66      (easy to assemble, perfect, yay)
--   repeat-cont        413042   14.88    13144.18 +- 6850.92      28603.17 +- 17366.51   (potential for consensus errors, no impact on assembly)
--   repeat-dove           857    0.03    28230.13 +- 23262.30     13834.25 +- 13066.09   (hard to assemble, likely won't assemble correctly or even at all)
--
--   span-repeat        471116   16.97    16913.34 +- 10869.32      6750.92 +- 7866.73    (read spans a large repeat, usually easy to assemble)
--   uniq-repeat-cont   614513   22.13    13917.04 +- 6841.91                             (should be uniquely placed, low potential for consensus errors, no impact on assembly)
--   uniq-repeat-dove    75145    2.71    27462.75 +- 16283.62                            (will end contigs, potential to misassemble)
--   uniq-anchor          5414    0.20    14838.73 +- 7721.39       3989.50 +- 4092.81    (repeat read, with unique section, probable bad read)

[UNITIGGING/ADJUSTMENT]
-- No report available.

[UNITIGGING/CONTIGS]
-- Found, in version 1, after unitig construction:
--   contigs:      15628 sequences, total length 1040237340 bp (including 309 repeats of total length 9025663 bp).
--   bubbles:      0 sequences, total length 0 bp.
--   unassembled:  714024 sequences, total length 9956827819 bp.
--
-- Contig sizes based on genome size 1gbp:
--
--            NG (bp)  LG (contigs)    sum (bp)
--         ----------  ------------  ----------
--     10      318252           251   100294830
--     20      237418           621   200171639
--     30      185277          1097   300146449
--     40      148117          1703   400115134
--     50      117619          2462   500089026
--     60       91956          3423   600049039
--     70       69873          4670   700006029
--     80       51152          6339   800041059
--     90       34247          8729   900015941
--    100       18285         12650  1000009816
--

[UNITIGGING/CONSENSUS]
-- Found, in version 2, after consensus generation:
--   contigs:      15628 sequences, total length 1043013647 bp (including 309 repeats of total length 9041122 bp).
--   bubbles:      0 sequences, total length 0 bp.
--   unassembled:  714024 sequences, total length 9956662647 bp.
--
-- Contig sizes based on genome size 1gbp:
--
--            NG (bp)  LG (contigs)    sum (bp)
--         ----------  ------------  ----------
--     10      319583           250   100308042
--     20      238658           617   200002412
--     30      186631          1090   300017659
--     40      149218          1692   400009521
--     50      118638          2446   500092655
--     60       92740          3399   600073014
--     70       70527          4635   700034380
--     80       51787          6286   800030370
--     90       34770          8646   900001060
--    100       18812         12495  1000002256
--

The unitigging/4-unitigger/001thr000.num000.log file is

INITIAL EDGES
-------- ----------------------------------------
 2557138 reads are contained
 5323066 reads have no best edges (singleton)
   66253 reads have only one best edge (spur)
            35108 are mutual best
  108081 reads have two best edges
            20840 have one mutual best edge
            77907 have two mutual best edges

ERROR RATES (4001955 samples)
-----------
mean   0.07781477 stddev 0.02621434 -> 0.23510080 fraction error =  23.510080% error
median 0.08080000 mad    0.02060000 -> 0.26404936 fraction error =  26.404936% error

EDGE FILTERING
-------- ------------------------------------------
 5326104 reads have a suspicious overlap pattern
       0 reads had edges filtered
                0 had one
                0 had two
   26879 reads have length incompatible edges
            18974 have one
             7905 have two

FINAL EDGES
-------- ----------------------------------------
 2557138 reads are contained
 5352690 reads have no best edges (singleton)
   79063 reads have only one best edge (spur)
            18126 are mutual best
   65647 reads have two best edges
             2988 have one mutual best edge
            50607 have two mutual best edges

[skoren]

Depending on how repetitive the plant is, a NG50 in the hundreds of kb is not unreasonable. Most of your reads are also relatively short (under 10kb). You can see from the logs there are a large fraction of reads contained in large 20kb repeats.

That said, your reads also look to be lower quality than normal. The median error rate is 8%, assuming you ran with the default error rate of 12% you will likely be missing true overlaps. I would suggest running two round (or more) of correction on the data, inputing the corrected reads as raw data again (with the parameters -correct corMhapSensivity=normal corOutCoverage=80). You could also try the latest base caller from nanopore to see if it improve the quality of the data. Then, for assembly don't use mhap for overlapping and use correctedErrorRate=0.15 ovlMerDistinct=0.975. You may also want to take a look at the FAQ for heterozygous genomes in case your genome is not inbred.