KMer Count is very skewed towards the beginning

[Furkan9015]

Hi,

I am using HERRO-corrected R9.4 data. It originally has a coverage of 450x and, after filtering for a min-length of 10kbp and error correction, it is down to 240x. Then, I take a subset of it with 35x coverage to use as the main input to the Hifiasm.

HERRO-corrected R9 reads were shown to be usable at around 30-35x coverage by the original HERRO paper. I use them with the raw ultra-long reads longer than 50kbp as the inputs to the Hifiasm.

However, assemblies are poor and the k-mer counts I have below are also interesting, what kind of a solution (such as parameter sweeps) do I need?

[M::ha_analyze_count] lowest: count[55] = 3749 [M::ha_analyze_count] highest: count[228] = 38565 [M::ha_hist_line] 2: ****************************************************************************************************> 45448636 [M::ha_hist_line] 3: ****************************************************************************************************> 16128660 [M::ha_hist_line] 4: ****************************************************************************************************> 7874831 [M::ha_hist_line] 5: ****************************************************************************************************> 4473368 [M::ha_hist_line] 6: ****************************************************************************************************> 2780220 [M::ha_hist_line] 7: ****************************************************************************************************> 1850257 [M::ha_hist_line] 8: ****************************************************************************************************> 1286884 [M::ha_hist_line] 9: ****************************************************************************************************> 929670 [M::ha_hist_line] 10: ****************************************************************************************************> 696630 [M::ha_hist_line] 11: ****************************************************************************************************> 530947 [M::ha_hist_line] 12: ****************************************************************************************************> 414721 [M::ha_hist_line] 13: ****************************************************************************************************> 329138 [M::ha_hist_line] 14: ****************************************************************************************************> 263659 [M::ha_hist_line] 15: ****************************************************************************************************> 214990 [M::ha_hist_line] 16: ****************************************************************************************************> 173913 [M::ha_hist_line] 17: ****************************************************************************************************> 145409 [M::ha_hist_line] 18: ****************************************************************************************************> 121472 [M::ha_hist_line] 19: ****************************************************************************************************> 103455 [M::ha_hist_line] 20: ****************************************************************************************************> 87593 [M::ha_hist_line] 21: ****************************************************************************************************> 75879 [M::ha_hist_line] 22: ****************************************************************************************************> 65062 [M::ha_hist_line] 23: ****************************************************************************************************> 55768 [M::ha_hist_line] 24: ****************************************************************************************************> 48143 [M::ha_hist_line] 25: ****************************************************************************************************> 42026 [M::ha_hist_line] 26: ************************************************************************************************** 37878 [M::ha_hist_line] 27: ************************************************************************************** 33327 [M::ha_hist_line] 28: **************************************************************************** 29335 [M::ha_hist_line] 29: ******************************************************************** 26116 [M::ha_hist_line] 30: ************************************************************* 23485 [M::ha_hist_line] 31: ****************************************************** 20697 [M::ha_hist_line] 32: ************************************************* 18771 [M::ha_hist_line] 33: ******************************************** 16944 [M::ha_hist_line] 34: *************************************** 15116 [M::ha_hist_line] 35: ************************************ 14044 [M::ha_hist_line] 36: ********************************** 12958 [M::ha_hist_line] 37: ****************************** 11644 [M::ha_hist_line] 38: **************************** 10761 [M::ha_hist_line] 39: ************************** 9862 [M::ha_hist_line] 40: ************************ 9271 [M::ha_hist_line] 41: ********************** 8385 [M::ha_hist_line] 42: ********************* 7960 [M::ha_hist_line] 43: ******************* 7326 [M::ha_hist_line] 44: ****************** 6847 [M::ha_hist_line] 45: **************** 6297 [M::ha_hist_line] 46: *************** 5842 [M::ha_hist_line] 47: ************** 5462 [M::ha_hist_line] 48: ************** 5262 [M::ha_hist_line] 49: ************* 5115 [M::ha_hist_line] 50: ************* 4880 [M::ha_hist_line] 51: ************ 4713 [M::ha_hist_line] 52: ************ 4470 [M::ha_hist_line] 53: *********** 4256 [M::ha_hist_line] 54: ********** 4023 [M::ha_hist_line] 55: ********** 3749 [M::ha_hist_line] 56: ********** 3780 [M::ha_hist_line] 57: ********** 3678 [M::ha_hist_line] 58: ********* 3629 [M::ha_hist_line] 59: ******** 3237 [M::ha_hist_line] 60: ******** 3188 [M::ha_hist_line] 61: ******** 3090 [M::ha_hist_line] 62: ******** 3050 [M::ha_hist_line] 63: ******** 2964 [M::ha_hist_line] 64: ******* 2862 [M::ha_hist_line] 65: ******* 2701 [M::ha_hist_line] 66: ******* 2707 [M::ha_hist_line] 67: ****** 2494 [M::ha_hist_line] 68: ****** 2478 [M::ha_hist_line] 69: ****** 2405 [M::ha_hist_line] 70: ****** 2400 [M::ha_hist_line] 71: ****** 2349 [M::ha_hist_line] 72: ****** 2202 [M::ha_hist_line] 73: ****** 2203 [M::ha_hist_line] 74: ***** 1952 [M::ha_hist_line] 75: ***** 2022 [M::ha_hist_line] 76: ***** 1920 [M::ha_hist_line] 77: ***** 1924 [M::ha_hist_line] 78: ***** 1927 [M::ha_hist_line] 79: ***** 1851 [M::ha_hist_line] 80: ***** 1852 [M::ha_hist_line] 81: ***** 1840 [M::ha_hist_line] 82: ***** 1766 [M::ha_hist_line] 83: ***** 1839 [M::ha_hist_line] 84: **** 1694 [M::ha_hist_line] 85: ***** 1738 [M::ha_hist_line] 86: ***** 1788 [M::ha_hist_line] 87: **** 1561 [M::ha_hist_line] 88: **** 1624 [M::ha_hist_line] 89: **** 1537 [M::ha_hist_line] 90: **** 1490 [M::ha_hist_line] 91: **** 1378 [M::ha_hist_line] 92: **** 1399 [M::ha_hist_line] 93: **** 1494 [M::ha_hist_line] 94: **** 1509 [M::ha_hist_line] 95: **** 1492 [M::ha_hist_line] 96: **** 1454 [M::ha_hist_line] 97: **** 1469 [M::ha_hist_line] 98: **** 1403 [M::ha_hist_line] 99: **** 1505 [M::ha_hist_line] 100: **** 1554 [M::ha_hist_line] 101: **** 1582 [M::ha_hist_line] 102: **** 1604 [M::ha_hist_line] 103: **** 1687 [M::ha_hist_line] 104: ***** 1738 [M::ha_hist_line] 105: ***** 1754 [M::ha_hist_line] 106: ***** 1778 [M::ha_hist_line] 107: ***** 1813 [M::ha_hist_line] 108: ***** 1932 [M::ha_hist_line] 109: ***** 1993 [M::ha_hist_line] 110: ***** 2013 [M::ha_hist_line] 111: ****** 2206 [M::ha_hist_line] 112: ****** 2419 [M::ha_hist_line] 113: ****** 2488 [M::ha_hist_line] 114: ******* 2528 [M::ha_hist_line] 115: ******* 2604 [M::ha_hist_line] 116: ******* 2710 [M::ha_hist_line] 117: ******* 2836 [M::ha_hist_line] 118: ******** 2962 [M::ha_hist_line] 119: ******** 3012 [M::ha_hist_line] 120: ******** 3042 [M::ha_hist_line] 121: ******** 3237 [M::ha_hist_line] 122: ********* 3507 [M::ha_hist_line] 123: ********* 3643 [M::ha_hist_line] 124: ********** 3716 [M::ha_hist_line] 125: ********** 3926 [M::ha_hist_line] 126: *********** 4145 [M::ha_hist_line] 127: *********** 4315 [M::ha_hist_line] 128: ************ 4510 [M::ha_hist_line] 129: ************ 4667 [M::ha_hist_line] 130: ************ 4746 [M::ha_hist_line] 131: ************ 4821 [M::ha_hist_line] 132: ************** 5209 [M::ha_hist_line] 133: ************* 5165 [M::ha_hist_line] 134: ************** 5343 [M::ha_hist_line] 135: ************** 5406 [M::ha_hist_line] 136: *************** 5693 [M::ha_hist_line] 137: *************** 5834 [M::ha_hist_line] 138: **************** 6116 [M::ha_hist_line] 139: **************** 6267 [M::ha_hist_line] 140: **************** 6330 [M::ha_hist_line] 141: ***************** 6579 [M::ha_hist_line] 142: ****************** 6801 [M::ha_hist_line] 143: ****************** 7063 [M::ha_hist_line] 144: ******************* 7191 [M::ha_hist_line] 145: ******************* 7363 [M::ha_hist_line] 146: ******************** 7752 [M::ha_hist_line] 147: ********************* 8149 [M::ha_hist_line] 148: ********************* 8287 [M::ha_hist_line] 149: ********************** 8454 [M::ha_hist_line] 150: *********************** 8734 [M::ha_hist_line] 151: *********************** 8859 [M::ha_hist_line] 152: ************************ 9139 [M::ha_hist_line] 153: ************************ 9368 [M::ha_hist_line] 154: ************************* 9540 [M::ha_hist_line] 155: ************************** 9883 [M::ha_hist_line] 156: ************************** 10129 [M::ha_hist_line] 157: **************************** 10720 [M::ha_hist_line] 158: **************************** 10855 [M::ha_hist_line] 159: ***************************** 11169 [M::ha_hist_line] 160: ***************************** 11362 [M::ha_hist_line] 161: ***************************** 11363 [M::ha_hist_line] 162: ******************************* 11901 [M::ha_hist_line] 163: ******************************* 12146 [M::ha_hist_line] 164: ******************************** 12217 [M::ha_hist_line] 165: ********************************* 12767 [M::ha_hist_line] 166: ********************************** 13177 [M::ha_hist_line] 167: *********************************** 13669 [M::ha_hist_line] 168: ************************************ 13880 [M::ha_hist_line] 169: ************************************* 14320 [M::ha_hist_line] 170: ************************************** 14508 [M::ha_hist_line] 171: *************************************** 14963 [M::ha_hist_line] 172: **************************************** 15517 [M::ha_hist_line] 173: ****************************************** 16027 [M::ha_hist_line] 174: ****************************************** 16278 [M::ha_hist_line] 175: ******************************************* 16627 [M::ha_hist_line] 176: ******************************************** 17081 [M::ha_hist_line] 177: ********************************************* 17447 [M::ha_hist_line] 178: *********************************************** 17949 [M::ha_hist_line] 179: ************************************************ 18668 [M::ha_hist_line] 180: ************************************************** 19237 [M::ha_hist_line] 181: *************************************************** 19597 [M::ha_hist_line] 182: **************************************************** 20078 [M::ha_hist_line] 183: ***************************************************** 20572 [M::ha_hist_line] 184: ******************************************************* 21020 [M::ha_hist_line] 185: ********************************************************* 21919 [M::ha_hist_line] 186: ********************************************************** 22330 [M::ha_hist_line] 187: *********************************************************** 22759 [M::ha_hist_line] 188: ************************************************************* 23477 [M::ha_hist_line] 189: *************************************************************** 24382 [M::ha_hist_line] 190: **************************************************************** 24619 [M::ha_hist_line] 191: ***************************************************************** 25133 [M::ha_hist_line] 192: ******************************************************************* 25698 [M::ha_hist_line] 193: ******************************************************************* 25955 [M::ha_hist_line] 194: ********************************************************************* 26793 [M::ha_hist_line] 195: ********************************************************************** 26882 [M::ha_hist_line] 196: *********************************************************************** 27565 [M::ha_hist_line] 197: ************************************************************************ 27888 [M::ha_hist_line] 198: ************************************************************************** 28600 [M::ha_hist_line] 199: **************************************************************************** 29369 [M::ha_hist_line] 200: ***************************************************************************** 29609 [M::ha_hist_line] 201: ****************************************************************************** 30215 [M::ha_hist_line] 202: ******************************************************************************* 30442 [M::ha_hist_line] 203: ********************************************************************************* 31240 [M::ha_hist_line] 204: ********************************************************************************** 31791 [M::ha_hist_line] 205: *********************************************************************************** 31877 [M::ha_hist_line] 206: ************************************************************************************ 32380 [M::ha_hist_line] 207: *************************************************************************************** 33445 [M::ha_hist_line] 208: **************************************************************************************** 33927 [M::ha_hist_line] 209: ***************************************************************************************** 34170 [M::ha_hist_line] 210: ****************************************************************************************** 34695 [M::ha_hist_line] 211: ******************************************************************************************** 35413 [M::ha_hist_line] 212: ******************************************************************************************* 35078 [M::ha_hist_line] 213: ******************************************************************************************** 35622 [M::ha_hist_line] 214: ******************************************************************************************** 35650 [M::ha_hist_line] 215: ********************************************************************************************** 36145 [M::ha_hist_line] 216: ************************************************************************************************ 36950 [M::ha_hist_line] 217: *********************************************************************************************** 36804 [M::ha_hist_line] 218: ************************************************************************************************* 37238 [M::ha_hist_line] 219: ************************************************************************************************** 37602 [M::ha_hist_line] 220: ************************************************************************************************* 37476 [M::ha_hist_line] 221: *************************************************************************************************** 38081 [M::ha_hist_line] 222: ************************************************************************************************** 37914 [M::ha_hist_line] 223: *************************************************************************************************** 38118 [M::ha_hist_line] 224: ************************************************************************************************** 37935 [M::ha_hist_line] 225: *************************************************************************************************** 38051 [M::ha_hist_line] 226: *************************************************************************************************** 38064 [M::ha_hist_line] 227: **************************************************************************************************** 38489 [M::ha_hist_line] 228: **************************************************************************************************** 38565 [M::ha_hist_line] 229: **************************************************************************************************** 38388 [M::ha_hist_line] 230: **************************************************************************************************** 38481 [M::ha_hist_line] 231: *************************************************************************************************** 37998 [M::ha_hist_line] 232: ************************************************************************************************** 37972 [M::ha_hist_line] 233: ************************************************************************************************** 37895 [M::ha_hist_line] 234: *************************************************************************************************** 38020 [M::ha_hist_line] 235: ************************************************************************************************** 37892 [M::ha_hist_line] 236: ************************************************************************************************* 37580 [M::ha_hist_line] 237: ************************************************************************************************* 37462 [M::ha_hist_line] 238: *********************************************************************************************** 36751 [M::ha_hist_line] 239: *********************************************************************************************** 36570 [M::ha_hist_line] 240: ********************************************************************************************** 36273 [M::ha_hist_line] 241: ******************************************************************************************** 35646 [M::ha_hist_line] 242: ******************************************************************************************** 35590 [M::ha_hist_line] 243: ******************************************************************************************* 34987 [M::ha_hist_line] 244: ****************************************************************************************** 34594 [M::ha_hist_line] 245: **************************************************************************************** 33839 [M::ha_hist_line] 246: ************************************************************************************** 33221 [M::ha_hist_line] 247: ************************************************************************************** 33033 [M::ha_hist_line] 248: ************************************************************************************ 32564 [M::ha_hist_line] 249: *********************************************************************************** 32017 [M::ha_hist_line] 250: ********************************************************************************** 31585 [M::ha_hist_line] 251: ******************************************************************************** 31026 [M::ha_hist_line] 252: ****************************************************************************** 30157 [M::ha_hist_line] 253: ***************************************************************************** 29693 [M::ha_hist_line] 254: *************************************************************************** 29114 [M::ha_hist_line] 255: ************************************************************************** 28394 [M::ha_hist_line] 256: ************************************************************************ 27674 [M::ha_hist_line] 257: ********************************************************************** 26806 [M::ha_hist_line] 258: ********************************************************************* 26420 [M::ha_hist_line] 259: ******************************************************************* 25779 [M::ha_hist_line] 260: ***************************************************************** 24996 [M::ha_hist_line] 261: **************************************************************** 24691 [M::ha_hist_line] 262: ************************************************************* 23562 [M::ha_hist_line] 263: *********************************************************** 22925 [M::ha_hist_line] 264: *********************************************************** 22653 [M::ha_hist_line] 265: ******************************************************** 21627 [M::ha_hist_line] 266: ******************************************************* 21266 [M::ha_hist_line] 267: ***************************************************** 20330 [M::ha_hist_line] 268: *************************************************** 19660 [M::ha_hist_line] 269: ************************************************* 18870 [M::ha_hist_line] 270: ************************************************ 18355 [M::ha_hist_line] 271: ********************************************* 17536 [M::ha_hist_line] 272: ******************************************** 16938 [M::ha_hist_line] 273: ******************************************* 16544 [M::ha_hist_line] 274: ***************************************** 15624 [M::ha_hist_line] 275: *************************************** 15089 [M::ha_hist_line] 276: ************************************** 14526 [M::ha_hist_line] 277: *********************************** 13610 [M::ha_hist_line] 278: ********************************** 13081 [M::ha_hist_line] 279: ********************************* 12543 [M::ha_hist_line] 280: ******************************* 11945 [M::ha_hist_line] 281: ****************************** 11577 [M::ha_hist_line] 282: ***************************** 11007 [M::ha_hist_line] 283: *************************** 10559 [M::ha_hist_line] 284: ************************** 10145 [M::ha_hist_line] 285: ************************* 9556 [M::ha_hist_line] 286: *********************** 9025 [M::ha_hist_line] 287: ********************** 8613 [M::ha_hist_line] 288: ********************* 8185 [M::ha_hist_line] 289: ******************** 7847 [M::ha_hist_line] 290: ******************* 7266 [M::ha_hist_line] 291: ****************** 6851 [M::ha_hist_line] 292: ***************** 6431 [M::ha_hist_line] 293: **************** 6285 [M::ha_hist_line] 294: *************** 5761 [M::ha_hist_line] 295: ************** 5589 [M::ha_hist_line] 296: ************** 5286 [M::ha_hist_line] 297: ************* 4833 [M::ha_hist_line] 298: ************ 4647 [M::ha_hist_line] 299: *********** 4255 [M::ha_hist_line] 300: *********** 4089 [M::ha_hist_line] 301: ********** 3797 [M::ha_hist_line] 302: ********* 3529 [M::ha_hist_line] 303: ******** 3269 [M::ha_hist_line] 304: ******** 3080 [M::ha_hist_line] 305: ******* 2837 [M::ha_hist_line] 306: ******* 2664 [M::ha_hist_line] 307: ****** 2473 [M::ha_hist_line] 308: ****** 2289 [M::ha_hist_line] 309: ****** 2172 [M::ha_hist_line] 310: ***** 1978 [M::ha_hist_line] 311: ***** 1852 [M::ha_hist_line] 312: ***** 1772 [M::ha_hist_line] 313: **** 1606 [M::ha_hist_line] 314: **** 1471 [M::ha_hist_line] 315: **** 1402 [M::ha_hist_line] 316: *** 1233 [M::ha_hist_line] 317: *** 1127 [M::ha_hist_line] 318: *** 1082 [M::ha_hist_line] 319: ** 959 [M::ha_hist_line] 320: ** 948 [M::ha_hist_line] 321: ** 793 [M::ha_hist_line] 322: ** 807 [M::ha_hist_line] 323: ** 733 [M::ha_hist_line] 324: ** 657 [M::ha_hist_line] 325: ** 590 [M::ha_hist_line] 326: * 534 [M::ha_hist_line] 327: * 496 [M::ha_hist_line] 328: * 472 [M::ha_hist_line] 329: * 471 [M::ha_hist_line] 330: * 413 [M::ha_hist_line] 331: * 356 [M::ha_hist_line] 332: * 342 [M::ha_hist_line] 333: * 308 [M::ha_hist_line] 334: * 300 [M::ha_hist_line] 335: * 259 [M::ha_hist_line] 336: * 259 [M::ha_hist_line] 337: * 220 [M::ha_hist_line] 338: * 245 [M::ha_hist_line] 339: * 199 [M::ha_hist_line] 340: * 200 [M::ha_hist_line] rest: ********************************************************************************************* 35872