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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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Suggested length cutoff: 0 bp #71

Closed ghost closed 4 years ago

ghost commented 4 years ago

Hello,

does it make sense that it suggests me a cutoff length of 0? Here are the results Thank you

[Read length histogram ('*' =~ 1514 reads)]
      0     999          0  
   1000    1999     264361  ******************************************************************************************************************************************************************************
   2000    2999     149321  **************************************************************************************************
   3000    3999     113546  **************************************************************************
   4000    4999      91689  ************************************************************
   5000    5999      73968  ************************************************
   6000    6999      64148  ******************************************
   7000    7999      60137  ***************************************
   8000    8999      60102  ***************************************
   9000    9999      58928  **************************************
  10000   10999      54866  ************************************
  11000   11999      50788  *********************************
  12000   12999      45890  ******************************
  13000   13999      41211  ***************************
  14000   14999      36878  ************************
  15000   15999      32546  *********************
  16000   16999      28783  *******************
  17000   17999      25099  ****************
  18000   18999      22211  **************
  19000   19999      19559  ************
  20000   20999      17174  ***********
  21000   21999      15034  *********
  22000   22999      13639  *********
  23000   23999      11983  *******
  24000   24999      10721  *******
  25000   25999       9578  ******
  26000   26999       8729  *****
  27000   27999       7814  *****
  28000   28999       7203  ****
  29000   29999       6624  ****
  30000   30999       6022  ***
  31000   31999       5709  ***
  32000   32999       5170  ***
  33000   33999       4856  ***
  34000   34999       4573  ***
  35000   35999       4223  **
  36000   36999       3921  **
  37000   37999       3723  **
  38000   38999       3535  **
  39000   39999       3308  **
  40000   40999       3205  **
  41000   41999       2952  *
  42000   42999       2814  *
  43000   43999       2637  *
  44000   44999       2605  *
  45000   45999       2392  *
  46000   46999       2328  *
  47000   47999       2252  *
  48000   48999       2083  *
  49000   49999       2025  *
  50000   50999       1862  *
  51000   51999       1822  *
  52000   52999       1719  *
  53000   53999       1573  *
  54000   54999       1610  *
  55000   55999       1553  *
  56000   56999       1432  
  57000   57999       1341  
  58000   58999       1329  
  59000   59999       1242  
  60000   60999       1166  
  61000   61999       1142  
  62000   62999       1069  
  63000   63999       1048  
  64000   64999        984  
  65000   65999        890  
  66000   66999        861  
  67000   67999        885  
  68000   68999        785  
  69000   69999        778  
  70000   70999        743  
  71000   71999        744  
  72000   72999        695  
  73000   73999        684  
  74000   74999        623  
  75000   75999        547  
  76000   76999        563  
  77000   77999        523  
  78000   78999        497  
  79000   79999        531  
  80000   80999        426  
  81000   81999        470  
  82000   82999        430  
  83000   83999        397  
  84000   84999        419  
  85000   85999        384  
  86000   86999        361  
  87000   87999        346  
  88000   88999        337  
  89000   89999        332  
  90000   90999        278  
  91000   91999        258  
  92000   92999        259  
  93000   93999        259  
  94000   94999        245  
  95000   95999        260  
  96000   96999        249  
  97000   97999        244  
  98000   98999        205  
  99000   99999        190  
 100000  100999        163  
 101000  101999        184  
 102000  102999        182  
 103000  103999        165  
 104000  104999        160  
 105000  105999        148  
 106000  106999        151  
 107000  107999        143  
 108000  108999        145  
 109000  109999        122  
 110000  110999        108  
 111000  111999        102  
 112000  112999        110  
 113000  113999        101  
 114000  114999        112  
 115000  115999        104  
 116000  116999         84  
 117000  117999         81  
 118000  118999         68  
 119000  119999         69  
 120000  120999         69  
 121000  121999         60  
 122000  122999         75  
 123000  123999         76  
 124000  124999         52  
 125000  125999         51  
 126000  126999         55  
 127000  127999         49  
 128000  128999         62  
 129000  129999         39  
 130000  130999         43  
 131000  131999         48  
 132000  132999         33  
 133000  133999         38  
 134000  134999         39  
 135000  135999         37  
 136000  136999         33  
 137000  137999         39  
 138000  138999         34  
 139000  139999         40  
 140000  140999         27  
 141000  141999         31  
 142000  142999         32  
 143000  143999         22  
 144000  144999         13  
 145000  145999         26  
 146000  146999         19  
 147000  147999         21  
 148000  148999         22  
 149000  149999         15  
 150000  150999         20  
 151000  151999         11  
 152000  152999         16  
 153000  153999         16  
 154000  154999         10  
 155000  155999         19  
 156000  156999         10  
 157000  157999         10  
 158000  158999         18  
 159000  159999         18  
 160000  160999         11  
 161000  161999         10  
 162000  162999          9  
 163000  163999         11  
 164000  164999          8  
 165000  165999          9  
 166000  166999          6  
 167000  167999          7  
 168000  168999          8  
 169000  169999          2  
 170000  170999          9  
 171000  171999          7  
 172000  172999          4  
 173000  173999          4  
 174000  174999          2  
 175000  175999          3  
 176000  176999          3  
 177000  177999          7  
 178000  178999          5  
 179000  179999          7  
 180000  180999          4  
 181000  181999          1  
 182000  182999          2  
 183000  183999          6  
 184000  184999          6  
 185000  185999          1  
 186000  186999          3  
 187000  187999          2  
 188000  188999          2  
 189000  189999          2  
 190000  190999          2  
 191000  191999          0  
 192000  192999          8  
 193000  193999          1  
 194000  194999          0  
 195000  195999          1  
 196000  196999          2  
 197000  197999          1  
 198000  198999          1  
 199000  199999          2  
 200000  200999          1  
 201000  201999          3  
 202000  202999          2  
 203000  203999          3  
 204000  204999          1  
 205000  205999          1  
 206000  206999          0  
 207000  207999          3  
 208000  208999          1  
 209000  209999          1  
 210000  210999          0  
 211000  211999          0  
 212000  212999          1  
 213000  213999          1  
 214000  214999          1  
 215000  215999          1  
 216000  216999          1  
 217000  217999          0  
 218000  218999          0  
 219000  219999          0  
 220000  220999          1  
 221000  221999          1  
 222000  222999          0  
 223000  223999          0  
 224000  224999          0  
 225000  225999          0  
 226000  226999          0  
 227000  227999          0  
 228000  228999          0  
 229000  229999          1  
 230000  230999          0  
 231000  231999          0  
 232000  232999          0  
 233000  233999          0  
 234000  234999          1  
 235000  235999          0  
 236000  236999          0  
 237000  237999          1  
 238000  238999          1  
 239000  239999          0  
 240000  240999          0  
 241000  241999          0  
 242000  242999          1  
 243000  243999          1  
 244000  244999          0  
 245000  245999          0  
 246000  246999          0  
 247000  247999          0  
 248000  248999          1  
 249000  249999          1  
 250000  250999          0  
 251000  251999          0  
 252000  252999          1  
 253000  253999          0  
 254000  254999          0  
 255000  255999          1  
 256000  256999          0  
 257000  257999          0  
 258000  258999          0  
 259000  259999          0  
 260000  260999          0  
 261000  261999          0  
 262000  262999          0  
 263000  263999          1  
 264000  264999          0  
 265000  265999          0  
 266000  266999          0  
 267000  267999          0  
 268000  268999          0  
 269000  269999          0  
 270000  270999          1  
 271000  271999          0  
 272000  272999          0  
 273000  273999          0  
 274000  274999          0  
 275000  275999          0  
 276000  276999          0  
 277000  277999          0  
 278000  278999          0  
 279000  279999          0  
 280000  280999          0  
 281000  281999          0  
 282000  282999          0  
 283000  283999          0  
 284000  284999          0  
 285000  285999          0  
 286000  286999          0  
 287000  287999          0  
 288000  288999          0  
 289000  289999          1  
 290000  290999          0  
 291000  291999          0  
 292000  292999          0  
 293000  293999          1  
 294000  294999          0  
 295000  295999          0  
 296000  296999          0  
 297000  297999          0  
 298000  298999          0  
 299000  299999          0  
 300000  300999          0  
 301000  301999          0  
 302000  302999          0  
 303000  303999          0  
 304000  304999          0  
 305000  305999          0  
 306000  306999          0  
 307000  307999          0  
 308000  308999          0  
 309000  309999          0  
 310000  310999          0  
 311000  311999          0  
 312000  312999          0  
 313000  313999          0  
 314000  314999          0  
 315000  315999          0  
 316000  316999          1  
 317000  317999          0  
 318000  318999          0  
 319000  319999          0  
 320000  320999          0  
 321000  321999          0  
 322000  322999          0  
 323000  323999          0  
 324000  324999          0  
 325000  325999          0  
 326000  326999          0  
 327000  327999          0  
 328000  328999          1  
 329000  329999          0  
 330000  330999          0  
 331000  331999          0  
 332000  332999          0  
 333000  333999          0  
 334000  334999          0  
 335000  335999          0  
 336000  336999          0  
 337000  337999          0  
 338000  338999          0  
 339000  339999          0  
 340000  340999          0  
 341000  341999          0  
 342000  342999          0  
 343000  343999          0  
 344000  344999          0  
 345000  345999          0  
 346000  346999          0  
 347000  347999          0  
 348000  348999          0  
 349000  349999          0  
 350000  350999          0  
 351000  351999          0  
 352000  352999          0  
 353000  353999          1  

[Read length stat]
Types            Count (#) Length (bp)
N10                  19605   66316
N20                  51314   45584
N30                  96113   32807
N40                 157266   24485
N50                 237178   19139
N60                 337957   15316
N70                 463928   12179
N80                 625810    9189
N90                 863481    5411

Types               Count (#)           Bases (bp)  Depth (X)
Raw                  52835547          28924641941       9.64
Filtered             51321025          11720485348       3.91
Clean                 1514522          17204156593       5.73

*Suggested length cutoff of reads (genome size: 3000000000, expected seed depth: 45) to be corrected: 0 bp
ghost commented 4 years ago

Okay, answered my own question, was given the wrong figure for genome size. Sorry