Assembly improvement

[pjm43]

I'm working on a plant species with moderately high repeat fraction (60%). I have approximately 90X coverage with Nanopore R9 1D reads. My initial assembly produced an N50 ~600 Kb, which I know is not bad, but I'm looking for ways I might improve it. I've seen in other posts that perhaps a couple rounds of correction (with the parameters -correct corMhapSensivity=normal corOutCoverage=80), followed by assembly with correctedErrorRate=0.15 ovlMerDistinct=0.975 was suggested. Would that be appropriate for this assembly? I've pasted in my original command, bottom portion of the final report and the unitigging/4-unitigger/001thr000.num000.log. Let me know if you need to see anything else.

Thanks for your help!

My original command:

canu -d canu_v1.8_Cwatsonii -p canu1.8_Cwatsonii genomeSize=500m maxMemory=500g maxThreads=24 corMhapSensitivity=normal corOutCoverage=40 \ merylMemory=500g merylThreads=24 ovlThreads=24 obtovlMemory=5g ovlMerThreshold=500 \ -nanopore-raw Final_watsonii_trimmed.q8_l2000.porechop.fq.gz

report:

report:

==========================================================================================
[UNITIGGING/OVERLAPS]
--   category            reads     %          read length        feature size or coverage  analysis
--   ----------------  -------  -------  ----------------------  ------------------------  --------------------
--   middle-missing        762    0.08    16633.16 +- 8429.90       1607.93 +- 1964.57    (bad trimming)
--   middle-hump            93    0.01     6588.52 +- 3791.93        778.74 +- 1293.99    (bad trimming)
--   no-5-prime           1884    0.19    13081.59 +- 6847.66        505.78 +- 1137.99    (bad trimming)
--   no-3-prime           1565    0.15    12971.92 +- 7071.60        451.00 +- 993.82     (bad trimming)
--
--   low-coverage         7035    0.69     7652.26 +- 4165.76          6.28 +- 2.63       (easy to assemble, potential for lower quality consensus)
--   unique             606789   59.75    18072.09 +- 6696.33         33.00 +- 6.95       (easy to assemble, perfect, yay)
--   repeat-cont        181053   17.83    16226.92 +- 7507.82       3272.53 +- 1699.60    (potential for consensus errors, no impact on assembly)
--   repeat-dove           520    0.05    29894.39 +- 17714.73      2066.97 +- 2409.62    (hard to assemble, likely won't assemble correctly or even at all)
--
--   span-repeat         39045    3.84    20998.46 +- 10307.43      5816.93 +- 4979.84    (read spans a large repeat, usually easy to assemble)
--   uniq-repeat-cont   141553   13.94    15337.16 +- 5384.26                             (should be uniquely placed, low potential for consensus errors, no impact on assembly)
--   uniq-repeat-dove    27997    2.76    24095.18 +- 10456.11                            (will end contigs, potential to misassemble)
--   uniq-anchor          7162    0.71    18174.99 +- 7184.36      10099.35 +- 7193.20    (repeat read, with unique section, probable bad read)

[UNITIGGING/ADJUSTMENT]
-- No report available.

[UNITIGGING/CONTIGS]
-- Found, in version 1, after unitig construction:
--   contigs:      3517 sequences, total length 536255101 bp (including 377 repeats of total length 8742209 bp).
--   bubbles:      0 sequences, total length 0 bp.
--   unassembled:  126153 sequences, total length 1987992988 bp.
--
-- Contig sizes based on genome size 500mbp:
--
--            NG (bp)  LG (contigs)    sum (bp)
--         ----------  ------------  ----------
--     10     2814540            13    51607288
--     20     1700537            38   101106989
--     30     1141962            74   150565492
--     40      817197           126   200006038
--     50      600580           199   250519651
--     60      442265           296   300268184
--     70      298594           432   350257657
--     80      186223           644   400069451
--     90      106562           995   450035317
--    100       40228          1753   500007493
--

[UNITIGGING/CONSENSUS]
-- Found, in version 2, after consensus generation:
--   contigs:      3517 sequences, total length 537158622 bp (including 377 repeats of total length 8726072 bp).
--   bubbles:      0 sequences, total length 0 bp.
--   unassembled:  126153 sequences, total length 1987986220 bp.
--
-- Contig sizes based on genome size 500mbp:
--
--            NG (bp)  LG (contigs)    sum (bp)
--         ----------  ------------  ----------
--     10     2824535            13    51752597
--     20     1705398            38   101395186
--     30     1145103            74   150963902
--     40      819608           126   200520991
--     50      602301           198   250535231
--     60      445368           294   300094489
--     70      302763           429   350153922
--     80      188856           640   400187312
--     90      107907           987   450086403
--    100       41262          1730   500015335

=========================================================================================

unitigging/4-unitigger/*001*thr000.num000.log

INITIAL EDGES
-------- ----------------------------------------
  930652 reads are contained
 2659687 reads have no best edges (singleton)
    6492 reads have only one best edge (spur)
             3832 are mutual best
   77787 reads have two best edges
             7440 have one mutual best edge
            64829 have two mutual best edges

ERROR RATES (1822937 samples)
-----------
mean   0.05778330 stddev 0.03005341 -> 0.23810375 fraction error =  23.810375% error
median 0.05560000 mad    0.02450000 -> 0.27354220 fraction error =  27.354220% error

EDGE FILTERING
-------- ------------------------------------------
 2671229 reads have a suspicious overlap pattern
       0 reads had edges filtered
                0 had one
                0 had two
   11582 reads have length incompatible edges
             6838 have one
             4744 have two

FINAL EDGES
-------- ----------------------------------------
  930652 reads are contained
 2661068 reads have no best edges (singleton)
   12168 reads have only one best edge (spur)
             2780 are mutual best
   70730 reads have two best edges
             2480 have one mutual best edge
            59206 have two mutual best edges

[skoren]

Your corrected read median rate is about what we normally see for nanopore data so I'm not sure multiple rounds would help. Instead of that, I would suggest using the latest nanopore flip-flop basecaller, that seems to boost accuracy at least on human/mammal data.

What does the histogram distribution look like? Is there a clear peak, does it look like your plant is heterozygous? If it is, you can also add the heterozygous parameters from the FAQ.

[pjm43]

Hmm, I'll look into the flip flop basecaller - we've been using guppy. Here's the full .report with the histograms - it should be a fairly homozygous species (inbreeder) - do you see any signs of heterozygousity?

[CORRECTION/READS]
--
-- In sequence store './canu1.8_Cwatsonii.seqStore':
--   Found 3674618 reads.
--   Found 45504226620 bases (91 times coverage).
--
--   Read length histogram (one '*' equals 19168.95 reads):
--        0   4999 362527 ******************
--     5000   9999 1062734 *******************************************************
--    10000  14999 1341827 **********************************************************************
--    15000  19999 544266 ****************************
--    20000  24999 191256 *********
--    25000  29999  80462 ****
--    30000  34999  39756 **
--    35000  39999  21384 *
--    40000  44999  11966 
--    45000  49999   7350 
--    50000  54999   4339 
--    55000  59999   2745 
--    60000  64999   1623 
--    65000  69999    961 
--    70000  74999    549 
--    75000  79999    334 
--    80000  84999    214 
--    85000  89999    124 
--    90000  94999     68 
--    95000  99999     46 
--   100000 104999     21 
--   105000 109999     20 
--   110000 114999     11 
--   115000 119999     10 
--   120000 124999      5 
--   125000 129999      7 
--   130000 134999      2 
--   135000 139999      3 
--   140000 144999      3 
--   145000 149999      0 
--   150000 154999      0 
--   155000 159999      2 
--   160000 164999      1 
--   165000 169999      0 
--   170000 174999      1 
--   175000 179999      0 
--   180000 184999      0 
--   185000 189999      0 
--   190000 194999      1

[CORRECTION/MERS]
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2 196614414 ****************************************                               0.1082 0.0087
--       3-     4 331108347 ********************************************************************   0.2060 0.0205
--       5-     7 336886262 ********************************************************************** 0.3625 0.0485
--       8-    11 264871097 *******************************************************                0.5206 0.0923
--      12-    16 185326314 **************************************                                 0.6473 0.1448
--      17-    22 124637569 *************************                                              0.7381 0.1986
--      23-    29  84745998 *****************                                                      0.8006 0.2494
--      30-    37  61508571 ************                                                           0.8440 0.2960
--      38-    46  49068501 **********                                                             0.8763 0.3404
--      47-    56  40076047 ********                                                               0.9024 0.3852
--      57-    67  30856753 ******                                                                 0.9237 0.4300
--      68-    79  22869582 ****                                                                   0.9401 0.4712
--      80-    92  17209377 ***                                                                    0.9523 0.5075
--      93-   106  13282535 **                                                                     0.9616 0.5396
--     107-   121  10346232 **                                                                     0.9687 0.5683
--     122-   137   8092640 *                                                                      0.9743 0.5940
--     138-   154   6395924 *                                                                      0.9786 0.6168
--     155-   172   5106579 *                                                                      0.9821 0.6372
--     173-   191   4114303                                                                        0.9849 0.6554
--     192-   211   3346296                                                                        0.9871 0.6718
--     212-   232   2751581                                                                        0.9889 0.6865
--     233-   254   2278472                                                                        0.9904 0.6999
--     255-   277   1906224                                                                        0.9917 0.7121
--     278-   301   1608964                                                                        0.9927 0.7232
--     302-   326   1362693                                                                        0.9936 0.7334
--     327-   352   1162661                                                                        0.9943 0.7428
--     353-   379    993926                                                                        0.9950 0.7515
--     380-   407    853895                                                                        0.9955 0.7595
--     408-   436    734321                                                                        0.9960 0.7669
--     437-   466    635831                                                                        0.9964 0.7737
--     467-   497    551923                                                                        0.9967 0.7800
--     498-   529    483288                                                                        0.9970 0.7858
--     530-   562    425269                                                                        0.9973 0.7913
--     563-   596    375077                                                                        0.9975 0.7964
--     597-   631    333745                                                                        0.9977 0.8012
--     632-   667    296306                                                                        0.9979 0.8057
--     668-   704    265592                                                                        0.9981 0.8100
--     705-   742    237097                                                                        0.9982 0.8140
--     743-   781    214416                                                                        0.9984 0.8178
--     782-   821    192922                                                                        0.9985 0.8214
--
--           0 (max occurrences)
-- 45254819515 (total mers, non-unique)
--  1816718316 (distinct mers, non-unique)
--           0 (unique mers)

[CORRECTION/LAYOUT]
--                             original      original
--                            raw reads     raw reads
--   category                w/overlaps  w/o/overlaps
--   -------------------- ------------- -------------
--   Number of Reads            3496253        178365
--   Number of Bases        44676732654     807353130
--   Coverage                    89.353         1.615
--   Median                       11490          3643
--   Mean                         12778          4526
--   N50                          13888          5119
--   Minimum                       2000             0
--   Maximum                     190190         45290
--   
--                                        --------corrected---------  ----------rescued----------
--                             evidence                     expected                     expected
--   category                     reads            raw     corrected            raw     corrected
--   -------------------- -------------  ------------- -------------  ------------- -------------
--   Number of Reads            3620404         972932        972932          43539         43539
--   Number of Bases        45005553344    20180544737   20000007715      384907673     376913877
--   Coverage                    90.011         40.361        40.000          0.770         0.754
--   Median                       11271          18229         18081           9028          8924
--   Mean                         12431          20741         20556           8840          8656
--   N50                          13819          19835         19629           9657          9584
--   Minimum                       2000          14420         14419           2001          1001
--   Maximum                     190190         173186        156754          50846         14419
--   
--                        --------uncorrected--------
--                                           expected
--   category                       raw     corrected
--   -------------------- ------------- -------------
--   Number of Reads            2658147       2658147
--   Number of Bases        24918633374   21056287888
--   Coverage                    49.837        42.113
--   Median                        9797          9433
--   Mean                          9374          7921
--   N50                          10822         11041
--   Minimum                          0             0
--   Maximum                     190190        188706
--   
--   Maximum Memory          2315925278

[TRIMMING/READS]
--
-- In sequence store './canu1.8_Cwatsonii.seqStore':
--   Found 1016421 reads.
--   Found 19952833652 bases (39.9 times coverage).
--
--   Read length histogram (one '*' equals 7199.87 reads):
--        0   4999   5131 
--     5000   9999  28382 ***
--    10000  14999 153023 *********************
--    15000  19999 503991 **********************************************************************
--    20000  24999 172908 ************************
--    25000  29999  72263 **********
--    30000  34999  35337 ****
--    35000  39999  19035 **
--    40000  44999  10590 *
--    45000  49999   6430 
--    50000  54999   3737 
--    55000  59999   2340 
--    60000  64999   1384 
--    65000  69999    803 
--    70000  74999    450 
--    75000  79999    260 
--    80000  84999    165 
--    85000  89999     73 
--    90000  94999     44 
--    95000  99999     29 
--   100000 104999     16 
--   105000 109999     10 
--   110000 114999      5 
--   115000 119999      5 
--   120000 124999      2 
--   125000 129999      5 
--   130000 134999      0 
--   135000 139999      0 
--   140000 144999      2 
--   145000 149999      0 
--   150000 154999      0 
--   155000 159999      1

[TRIMMING/MERS]
--
--  22-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2 305927822 ********************************************************************** 0.3211 0.0352
--       3-     4 193748129 ********************************************                           0.4517 0.0567
--       5-     7 101345153 ***********************                                                0.5718 0.0857
--       8-    11  59785945 *************                                                          0.6511 0.1154
--      12-    16  41872965 *********                                                              0.7043 0.1455
--      17-    22  37736130 ********                                                               0.7446 0.1783
--      23-    29  56739955 ************                                                           0.7842 0.2229
--      30-    37  80370823 ******************                                                     0.8475 0.3175
--      38-    46  43273859 *********                                                              0.9295 0.4719
--      47-    56   9114318 **                                                                     0.9684 0.5613
--      57-    67   5212685 *                                                                      0.9767 0.5848
--      68-    79   4145726                                                                        0.9821 0.6034
--      80-    92   2415494                                                                        0.9862 0.6202
--      93-   106   1876864                                                                        0.9887 0.6318
--     107-   121   1382352                                                                        0.9906 0.6424
--     122-   137   1068747                                                                        0.9920 0.6513
--     138-   154    867780                                                                        0.9931 0.6592
--     155-   172    730396                                                                        0.9940 0.6664
--     173-   191    627446                                                                        0.9948 0.6732
--     192-   211    537982                                                                        0.9954 0.6797
--     212-   232    435028                                                                        0.9960 0.6859
--     233-   254    352033                                                                        0.9964 0.6914
--     255-   277    295788                                                                        0.9968 0.6963
--     278-   301    252535                                                                        0.9971 0.7008
--     302-   326    218702                                                                        0.9974 0.7050
--     327-   352    191725                                                                        0.9976 0.7090
--     353-   379    169811                                                                        0.9978 0.7127
--     380-   407    149809                                                                        0.9980 0.7162
--     408-   436    133504                                                                        0.9981 0.7196
--     437-   466    118422                                                                        0.9983 0.7229
--     467-   497    105796                                                                        0.9984 0.7259
--     498-   529     94626                                                                        0.9985 0.7289
--     530-   562     84859                                                                        0.9986 0.7316
--     563-   596     76531                                                                        0.9987 0.7343
--     597-   631     70189                                                                        0.9988 0.7369
--     632-   667     63708                                                                        0.9988 0.7393
--     668-   704     58743                                                                        0.9989 0.7417
--     705-   742     53039                                                                        0.9990 0.7440
--     743-   781     48739                                                                        0.9990 0.7462
--     782-   821     45176                                                                        0.9991 0.7484
--
--           0 (max occurrences)
-- 17362747871 (total mers, non-unique)
--   952639470 (distinct mers, non-unique)
--           0 (unique mers)

[TRIMMING/TRIMMING]
--  PARAMETERS:
--  ----------
--     1000    (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:
--  -----------
--  3674618 reads  19952833652 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:
--  ------------
--  826131 reads  14459470441 bases (trimmed reads output)
--  189483 reads   3376897607 bases (reads with no change, kept as is)
--  2658532 reads      1691483 bases (reads with no overlaps, deleted)
--     472 reads      3250716 bases (reads with short trimmed length, deleted)
--  
--  TRIMMING DETAILS:
--  ----------------
--  516307 reads   1044594022 bases (bases trimmed from the 5' end of a read)
--  701024 reads   1066929383 bases (bases trimmed from the 3' end of a read)

[TRIMMING/SPLITTING]
--  PARAMETERS:
--  ----------
--     1000    (reads trimmed below this many bases are deleted)
--   0.1200    (use overlaps at or below this fraction error)
--  INPUT READS:
--  -----------
--  1015614 reads  19947891453 bases (reads processed)
--  2659004 reads      4942199 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)
--      77 reads      1168549 bases (no coverage after adjusting for trimming done already)
--       0 reads            0 bases (processed for chimera)
--       0 reads            0 bases (processed for spur)
--  1015537 reads  19946722904 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)
--     995 reads         1004 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)
--    1004 reads       404327 bases (size of subread signal)
--  
--  TRIMMING:
--  --------
--     369 reads      2803988 bases (trimmed from the 5' end of the read)
--     627 reads      5902955 bases (trimmed from the 3' end of the read)

[UNITIGGING/READS]
--
-- In sequence store './canu1.8_Cwatsonii.seqStore':
--   Found 1015613 reads.
--   Found 17827660343 bases (35.65 times coverage).
--
--   Read length histogram (one '*' equals 6129.84 reads):
--        0   4999  13776 **
--     5000   9999  87295 **************
--    10000  14999 244114 ***************************************
--    15000  19999 429089 **********************************************************************
--    20000  24999 133921 *********************
--    25000  29999  51809 ********
--    30000  34999  24981 ****
--    35000  39999  13230 **
--    40000  44999   7209 *
--    45000  49999   4397 
--    50000  54999   2466 
--    55000  59999   1485 
--    60000  64999    856 
--    65000  69999    478 
--    70000  74999    261 
--    75000  79999    117 
--    80000  84999     78 
--    85000  89999     23 
--    90000  94999     16 
--    95000  99999     10 
--   100000 104999      0 
--   105000 109999      1 
--   110000 114999      0 
--   115000 119999      1

[UNITIGGING/MERS]
--
--  22-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2 255642300 ********************************************************************** 0.3042 0.0323
--       3-     4 165368556 *********************************************                          0.4301 0.0524
--       5-     7  88346759 ************************                                               0.5475 0.0797
--       8-    11  53455256 **************                                                         0.6265 0.1084
--      12-    16  38888289 **********                                                             0.6808 0.1382
--      17-    22  38023505 **********                                                             0.7237 0.1720
--      23-    29  60413087 ****************                                                       0.7698 0.2224
--      30-    37  77033475 *********************                                                  0.8457 0.3321
--      38-    46  35563108 *********                                                              0.9331 0.4909
--      47-    56   7577945 **                                                                     0.9688 0.5701
--      57-    67   4837427 *                                                                      0.9768 0.5921
--      68-    79   3509373                                                                        0.9825 0.6109
--      80-    92   2107339                                                                        0.9865 0.6264
--      93-   106   1633577                                                                        0.9889 0.6376
--     107-   121   1188442                                                                        0.9908 0.6477
--     122-   137    930874                                                                        0.9922 0.6561
--     138-   154    761609                                                                        0.9932 0.6636
--     155-   172    645629                                                                        0.9941 0.6706
--     173-   191    558844                                                                        0.9949 0.6772
--     192-   211    456453                                                                        0.9956 0.6836
--     212-   232    366801                                                                        0.9961 0.6893
--     233-   254    297116                                                                        0.9965 0.6944
--     255-   277    250906                                                                        0.9969 0.6989
--     278-   301    214810                                                                        0.9972 0.7031
--     302-   326    186711                                                                        0.9974 0.7070
--     327-   352    163903                                                                        0.9976 0.7107
--     353-   379    146136                                                                        0.9978 0.7142
--     380-   407    128174                                                                        0.9980 0.7176
--     408-   436    113587                                                                        0.9982 0.7208
--     437-   466    100354                                                                        0.9983 0.7238
--     467-   497     90092                                                                        0.9984 0.7266
--     498-   529     80509                                                                        0.9985 0.7294
--     530-   562     71583                                                                        0.9986 0.7320
--     563-   596     65735                                                                        0.9987 0.7344
--     597-   631     59515                                                                        0.9988 0.7368
--     632-   667     54607                                                                        0.9989 0.7391
--     668-   704     49469                                                                        0.9989 0.7414
--     705-   742     46013                                                                        0.9990 0.7435
--     743-   781     41882                                                                        0.9990 0.7456
--     782-   821     38405                                                                        0.9991 0.7476
--
--           0 (max occurrences)
-- 15825236058 (total mers, non-unique)
--   840241886 (distinct mers, non-unique)
--           0 (unique mers)

[UNITIGGING/OVERLAPS]
--   category            reads     %          read length        feature size or coverage  analysis
--   ----------------  -------  -------  ----------------------  ------------------------  --------------------
--   middle-missing        762    0.08    16633.16 +- 8429.90       1607.93 +- 1964.57    (bad trimming)
--   middle-hump            93    0.01     6588.52 +- 3791.93        778.74 +- 1293.99    (bad trimming)
--   no-5-prime           1884    0.19    13081.59 +- 6847.66        505.78 +- 1137.99    (bad trimming)
--   no-3-prime           1565    0.15    12971.92 +- 7071.60        451.00 +- 993.82     (bad trimming)
--   
--   low-coverage         7035    0.69     7652.26 +- 4165.76          6.28 +- 2.63       (easy to assemble, potential for lower quality consensus)
--   unique             606789   59.75    18072.09 +- 6696.33         33.00 +- 6.95       (easy to assemble, perfect, yay)
--   repeat-cont        181053   17.83    16226.92 +- 7507.82       3272.53 +- 1699.60    (potential for consensus errors, no impact on assembly)
--   repeat-dove           520    0.05    29894.39 +- 17714.73      2066.97 +- 2409.62    (hard to assemble, likely won't assemble correctly or even at all)
--   
--   span-repeat         39045    3.84    20998.46 +- 10307.43      5816.93 +- 4979.84    (read spans a large repeat, usually easy to assemble)
--   uniq-repeat-cont   141553   13.94    15337.16 +- 5384.26                             (should be uniquely placed, low potential for consensus errors, no impact on assembly)
--   uniq-repeat-dove    27997    2.76    24095.18 +- 10456.11                            (will end contigs, potential to misassemble)
--   uniq-anchor          7162    0.71    18174.99 +- 7184.36      10099.35 +- 7193.20    (repeat read, with unique section, probable bad read)

[UNITIGGING/ADJUSTMENT]
-- No report available.

[UNITIGGING/CONTIGS]
-- Found, in version 1, after unitig construction:
--   contigs:      3517 sequences, total length 536255101 bp (including 377 repeats of total length 8742209 bp).
--   bubbles:      0 sequences, total length 0 bp.
--   unassembled:  126153 sequences, total length 1987992988 bp.
--
-- Contig sizes based on genome size 500mbp:
--
--            NG (bp)  LG (contigs)    sum (bp)
--         ----------  ------------  ----------
--     10     2814540            13    51607288
--     20     1700537            38   101106989
--     30     1141962            74   150565492
--     40      817197           126   200006038
--     50      600580           199   250519651
--     60      442265           296   300268184
--     70      298594           432   350257657
--     80      186223           644   400069451
--     90      106562           995   450035317
--    100       40228          1753   500007493
--

[UNITIGGING/CONSENSUS]
-- Found, in version 2, after consensus generation:
--   contigs:      3517 sequences, total length 537158622 bp (including 377 repeats of total length 8726072 bp).
--   bubbles:      0 sequences, total length 0 bp.
--   unassembled:  126153 sequences, total length 1987986220 bp.
--
-- Contig sizes based on genome size 500mbp:
--
--            NG (bp)  LG (contigs)    sum (bp)
--         ----------  ------------  ----------
--     10     2824535            13    51752597
--     20     1705398            38   101395186
--     30     1145103            74   150963902
--     40      819608           126   200520991
--     50      602301           198   250535231
--     60      445368           294   300094489
--     70      302763           429   350153922
--     80      188856           640   400187312
--     90      107907           987   450086403
--    100       41262          1730   500015335
--

[skoren]

It looks pretty homozygous from the plots so no need to include the het parameters.