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?
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