How to set --hom-cov to homozygous coverage peak correctly?

[liyhui123]

Hello, I have a diploid plant of ~ 1000 MB haploid size, and we have ~65x hifi coverage of the haploid genome, meaning >30x per haplotype. The quality of the k-mer histogram is not good, hifisam was unable to correctly identify potential homozygous peaks correctly, and the initial assembled contig N50 was very low (approximately 2.8Mb for untyped, and approximately 1Mb for each haplotype). Through the alignment results of Blastn, I determined that there was no contamination of the hifi data. According to the log, I set --hom-cov 42, but no real change in the result. How to set --hom-cov to homozygous coverage peak correctly? Should I increase the amount of hifi data? I would appreciate any other better suggestions. Thanks! This is part of the log. [M::ha_analyze_count] lowest: count[5] = 8999756 [M::ha_analyze_count] highest: count[11] = 10360280 [M::ha_hist_line] 2: *************************************************************************************************> 18909787 [M::ha_hist_line] 3: ***************************************************************************************** 9229832 [M::ha_hist_line] 4: ********************************************************************************** 8521897 [M::ha_hist_line] 5: *************************************************************************************** 8999756 [M::ha_hist_line] 6: ********************************************************************************************* 9620994 [M::ha_hist_line] 7: *********************************************************************************************** 9891080 [M::ha_hist_line] 8: *************************************************************************************************** 10205215 [M::ha_hist_line] 9: ************************************************************************************************** 10190218 [M::ha_hist_line] 10: *************************************************************************************************** 10304830 [M::ha_hist_line] 11: **************************************************************************************************** 10360280 [M::ha_hist_line] 12: *************************************************************************************************** 10270415 [M::ha_hist_line] 13: ************************************************************************************************** 10156451 [M::ha_hist_line] 14: ************************************************************************************************* 10071596 [M::ha_hist_line] 15: ************************************************************************************************ 9943329 [M::ha_hist_line] 16: ********************************************************************************************** 9763759 [M::ha_hist_line] 17: *********************************************************************************************** 9844973 [M::ha_hist_line] 18: ********************************************************************************************** 9752398 [M::ha_hist_line] 19: ********************************************************************************************** 9700835 [M::ha_hist_line] 20: ******************************************************************************************** 9576034 [M::ha_hist_line] 21: ******************************************************************************************* 9465831 [M::ha_hist_line] 22: ******************************************************************************************* 9463375 [M::ha_hist_line] 23: ******************************************************************************************* 9376402 [M::ha_hist_line] 24: ****************************************************************************************** 9358718 [M::ha_hist_line] 25: ****************************************************************************************** 9311239 [M::ha_hist_line] 26: ****************************************************************************************** 9282690 [M::ha_hist_line] 27: ****************************************************************************************** 9326489 [M::ha_hist_line] 28: ****************************************************************************************** 9284747 [M::ha_hist_line] 29: ***************************************************************************************** 9265633 [M::ha_hist_line] 30: ****************************************************************************************** 9366276 [M::ha_hist_line] 31: ******************************************************************************************* 9444382 [M::ha_hist_line] 32: ********************************************************************************************* 9648184 [M::ha_hist_line] 33: ********************************************************************************************** 9700708 [M::ha_hist_line] 34: ********************************************************************************************** 9773103 [M::ha_hist_line] 35: *********************************************************************************************** 9833881 [M::ha_hist_line] 36: ************************************************************************************************ 9959200 [M::ha_hist_line] 37: ************************************************************************************************ 9989391 [M::ha_hist_line] 38: ************************************************************************************************ 9970453 [M::ha_hist_line] 39: ************************************************************************************************ 9986746 [M::ha_hist_line] 40: ************************************************************************************************* 10002148 [M::ha_hist_line] 41: ************************************************************************************************* 10004421 [M::ha_hist_line] 42: ************************************************************************************************* 10032727 [M::ha_hist_line] 43: ************************************************************************************************* 10040667 [M::ha_hist_line] 44: ************************************************************************************************* 10011410 [M::ha_hist_line] 45: ************************************************************************************************ 9969910 [M::ha_hist_line] 46: *********************************************************************************************** 9827777 [M::ha_hist_line] 47: ********************************************************************************************* 9661976 [M::ha_hist_line] 48: ******************************************************************************************* 9465458 [M::ha_hist_line] 49: ***************************************************************************************** 9262714 [M::ha_hist_line] 50: *************************************************************************************** 9014960 [M::ha_hist_line] 51: ************************************************************************************* 8832578 [M::ha_hist_line] 52: *********************************************************************************** 8563710 [M::ha_hist_line] 53: ******************************************************************************** 8241291 [M::ha_hist_line] 54: ***************************************************************************** 7946378 [M::ha_hist_line] 55: ************************************************************************* 7609927 [M::ha_hist_line] 56: ********************************************************************** 7278245 [M::ha_hist_line] 57: ******************************************************************* 6892516 [M::ha_hist_line] 58: *************************************************************** 6505274 [M::ha_hist_line] 59: *********************************************************** 6159180 [M::ha_hist_line] 60: ******************************************************** 5803273 [M::ha_hist_line] 61: ***************************************************** 5519339 [M::ha_hist_line] 62: *************************************************** 5248287 [M::ha_hist_line] 63: ************************************************ 4990333 [M::ha_hist_line] 64: ********************************************** 4752589 [M::ha_hist_line] 65: ******************************************** 4534879 [M::ha_hist_line] 66: ***************************************** 4280300 [M::ha_hist_line] 67: *************************************** 4085088 [M::ha_hist_line] 68: ************************************** 3903847 [M::ha_hist_line] 69: ************************************* 3789624 [M::ha_hist_line] 70: *********************************** 3645935 [M::ha_hist_line] 71: ********************************** 3549931 [M::ha_hist_line] 72: ********************************* 3432400 [M::ha_hist_line] 73: ******************************** 3305446 [M::ha_hist_line] 74: ******************************* 3207555 [M::ha_hist_line] 75: ****************************** 3140617 [M::ha_hist_line] 76: ****************************** 3088777 [M::ha_hist_line] 77: ***************************** 3040061 [M::ha_hist_line] 78: ***************************** 2993773 [M::ha_hist_line] 79: ***************************** 2961653 [M::ha_hist_line] 80: **************************** 2933302 [M::ha_hist_line] 81: **************************** 2904616 [M::ha_hist_line] 82: **************************** 2892131 [M::ha_hist_line] 83: **************************** 2875775 [M::ha_hist_line] 84: *************************** 2843367 [M::ha_hist_line] 85: *************************** 2842264 [M::ha_hist_line] 86: *************************** 2828966 [M::ha_hist_line] 87: *************************** 2807063 [M::ha_hist_line] 88: *************************** 2795906 [M::ha_hist_line] 89: *************************** 2800400 [M::ha_hist_line] 90: *************************** 2769053 [M::ha_hist_line] 91: ************************** 2727407 [M::ha_hist_line] 92: ************************** 2673741 [M::ha_hist_line] 93: ************************* 2634428 [M::ha_hist_line] 94: ************************* 2600925 [M::ha_hist_line] 95: ************************* 2564587 [M::ha_hist_line] 96: ************************ 2523369 [M::ha_hist_line] 97: ************************ 2482584 [M::ha_hist_line] 98: ************************ 2444718 [M::ha_hist_line] 99: *********************** 2394272 [M::ha_hist_line] 100: *********************** 2350709 [M::ha_hist_line] 101: ********************** 2305963 [M::ha_hist_line] 102: ********************** 2250433 [M::ha_hist_line] 103: ********************* 2187436 [M::ha_hist_line] 104: ******************** 2099299 [M::ha_hist_line] 105: ******************** 2031613 [M::ha_hist_line] 106: ******************* 1954647 [M::ha_hist_line] 107: ****************** 1882379 [M::ha_hist_line] 108: ****************** 1819131 [M::ha_hist_line] 109: ***************** 1763187 [M::ha_hist_line] 110: **************** 1686277 [M::ha_hist_line] 111: **************** 1623724 [M::ha_hist_line] 112: *************** 1577565 [M::ha_hist_line] 113: *************** 1523953 [M::ha_hist_line] 114: ************** 1445329 [M::ha_hist_line] 115: ************* 1366962 [M::ha_hist_line] 116: ************* 1303118 [M::ha_hist_line] 117: ************ 1238605 [M::ha_hist_line] 118: *********** 1179281 [M::ha_hist_line] 119: *********** 1099641 [M::ha_hist_line] 120: ********** 1044394 [M::ha_hist_line] 121: ********** 990807 [M::ha_hist_line] 122: ********* 926222 [M::ha_hist_line] 123: ******** 868606 [M::ha_hist_line] 124: ******** 806122 [M::ha_hist_line] 125: ******* 759857 [M::ha_hist_line] 126: ******* 701356 [M::ha_hist_line] 127: ****** 653815 [M::ha_hist_line] 128: ****** 616961 [M::ha_hist_line] 129: ****** 581524 [M::ha_hist_line] 130: ***** 546435 [M::ha_hist_line] 131: ***** 504537 [M::ha_hist_line] 132: ***** 475643 [M::ha_hist_line] 133: **** 443161 [M::ha_hist_line] 134: **** 415033 [M::ha_hist_line] 135: **** 382702 [M::ha_hist_line] 136: *** 359731 [M::ha_hist_line] 137: *** 336684 [M::ha_hist_line] 138: *** 312425 [M::ha_hist_line] 139: *** 293400 [M::ha_hist_line] 140: *** 278959 [M::ha_hist_line] 141: *** 262112 [M::ha_hist_line] 142: ** 244256 [M::ha_hist_line] 143: ** 229849 [M::ha_hist_line] 144: ** 220475 [M::ha_hist_line] 145: ** 209480 [M::ha_hist_line] 146: ** 199336 [M::ha_hist_line] 147: ** 189459 [M::ha_hist_line] 148: ** 183260 [M::ha_hist_line] 149: ** 174855 [M::ha_hist_line] 150: ** 170160 [M::ha_hist_line] 151: ** 162824 [M::ha_hist_line] 152: ** 160653 [M::ha_hist_line] 153: * 155054 [M::ha_hist_line] 154: * 149755 [M::ha_hist_line] 155: * 144327 [M::ha_hist_line] 156: * 144305 [M::ha_hist_line] 157: * 141551 [M::ha_hist_line] 158: * 143503 [M::ha_hist_line] 159: * 139733 [M::ha_hist_line] 160: * 135735 [M::ha_hist_line] 161: * 131787 [M::ha_hist_line] 162: * 129034 [M::ha_hist_line] 163: * 129297 [M::ha_hist_line] 164: * 125293 [M::ha_hist_line] 165: * 120801 [M::ha_hist_line] 166: * 117096 [M::ha_hist_line] 167: * 114649 [M::ha_hist_line] 168: * 115608 [M::ha_hist_line] 169: * 111749 [M::ha_hist_line] 170: * 109304 [M::ha_hist_line] 171: * 110428 [M::ha_hist_line] 172: * 108564 [M::ha_hist_line] 173: * 105503 [M::ha_hist_line] 174: * 103300 [M::ha_hist_line] 175: * 104239 [M::ha_hist_line] 176: * 101628 [M::ha_hist_line] 177: * 99475 [M::ha_hist_line] 178: * 99263 [M::ha_hist_line] 179: * 96208 [M::ha_hist_line] 180: * 95820 [M::ha_hist_line] 181: * 93941 [M::ha_hist_line] 182: * 91540 [M::ha_hist_line] 183: * 94561 [M::ha_hist_line] 184: * 89967 [M::ha_hist_line] 185: * 90544 [M::ha_hist_line] 186: * 88444 [M::ha_hist_line] 187: * 87948 [M::ha_hist_line] 188: * 84888 [M::ha_hist_line] 189: * 84654 [M::ha_hist_line] 190: * 81990 [M::ha_hist_line] 191: * 83186 [M::ha_hist_line] 192: * 80641 [M::ha_hist_line] 193: * 79374 [M::ha_hist_line] 194: * 80482 [M::ha_hist_line] 195: * 78864 [M::ha_hist_line] 196: * 78047 [M::ha_hist_line] 197: * 78435 [M::ha_hist_line] 198: * 76847 [M::ha_hist_line] 199: * 76900 [M::ha_hist_line] 200: * 76534 [M::ha_hist_line] 201: * 74141 [M::ha_hist_line] 202: * 73438 [M::ha_hist_line] 203: * 72840 [M::ha_hist_line] 204: * 71075 [M::ha_hist_line] 205: * 69273 [M::ha_hist_line] 206: * 68268 [M::ha_hist_line] 207: * 68014 [M::ha_hist_line] 208: * 67471 [M::ha_hist_line] 209: * 65562 [M::ha_hist_line] 210: * 64746 [M::ha_hist_line] 211: * 63816 [M::ha_hist_line] 212: * 62840 [M::ha_hist_line] 213: * 61483 [M::ha_hist_line] 214: * 60948 [M::ha_hist_line] 215: * 60385 [M::ha_hist_line] 216: * 60403 [M::ha_hist_line] 217: * 58928 [M::ha_hist_line] 218: * 57972 [M::ha_hist_line] 219: * 59188 [M::ha_hist_line] 220: * 56852 [M::ha_hist_line] 221: * 55911 [M::ha_hist_line] 222: * 54565 [M::ha_hist_line] 223: * 55051 [M::ha_hist_line] 224: * 55397 [M::ha_hist_line] 225: * 54514 [M::ha_hist_line] 226: * 53752 [M::ha_hist_line] 227: * 51973 [M::ha_hist_line] rest: ************************************************************************************* 8786130 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: none [M::ha_ft_gen] peak_hom: 11; peak_het: -1 [M::ha_ct_shrink::6814.6721.95] ==> counted 232977800 distinct minimizer k-mers [M::ha_ft_gen::6844.593[email protected]] ==> filtered out 232977800 k-mers occurring 55 or more times [M::ha_opt_update_cov] updated max_n_chain to 100 [M::yak_count] collected 119436745 minimizers [M::yak_count] collected 1070387661 minimizers [M::ha_pt_gen::12941.3522.05] ==> counted 85172261 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[7] = 564040

[chhylp123]

Is that a fish? I'm not sure if this issue is helpful for your case (see: https://github.com/chhylp123/hifiasm/issues/511#issuecomment-1696932392).

[liyhui123]

Is that a fish? I'm not sure if this issue is helpful for your case (see: #511 (comment)).

This is a kind of forest tree, but I'm not sure if it has as many microsatellite sequences as a fish does.