hifiasm
hifiasm copied to clipboard
Read error correction does not reduce the number of kmers present once, twice or three times
I try to assemble herro error corrected reads with hifiasm 0.19.8
But the number of kmers seen a low number of times does not decrease as expected
Initial histogram in the log
[M::ha_hist_line] 2: ****************************************************************************************************> 107716610 [M::ha_hist_line] 3: ****************************************************************************************************> 30996780 [M::ha_hist_line] 4: ************************************************************** 15593515 [M::ha_hist_line] 5: ********************************************* 11280672 [M::ha_hist_line] 6: ****************************************** 10378745 [M::ha_hist_line] 7: ******************************************** 10969244 [M::ha_hist_line] 8: ************************************************** 12440832 [M::ha_hist_line] 9: ********************************************************* 14313356 [M::ha_hist_line] 10: ****************************************************************** 16548878 [M::ha_hist_line] 11: *************************************************************************** 18834001 [M::ha_hist_line] 12: ************************************************************************************ 20983530 [M::ha_hist_line] 13: ******************************************************************************************* 22728212 [M::ha_hist_line] 14: ************************************************************************************************ 24067655 [M::ha_hist_line] 15: **************************************************************************************************** 24853609 [M::ha_hist_line] 16: **************************************************************************************************** 24957299 [M::ha_hist_line] 17: *************************************************************************************************** 24619025 [M::ha_hist_line] 18: *********************************************************************************************** 23715443 [M::ha_hist_line] 19: ****************************************************************************************** 22573874 [M::ha_hist_line] 20: ************************************************************************************* 21273382 [M::ha_hist_line] 21: ******************************************************************************** 19908321 [M::ha_hist_line] 22: *************************************************************************** 18789819 [M::ha_hist_line] 23: ************************************************************************ 18034450 [M::ha_hist_line] 24: ********************************************************************** 17581256 [M::ha_hist_line] 25: ********************************************************************** 17553086 [M::ha_hist_line] 26: ************************************************************************ 17887681 [M::ha_hist_line] 27: ************************************************************************** 18591686 [M::ha_hist_line] 28: ****************************************************************************** 19396013 [M::ha_hist_line] 29: ********************************************************************************* 20301932 [M::ha_hist_line] 30: ************************************************************************************ 21087688 [M::ha_hist_line] 31: *************************************************************************************** 21817734 [M::ha_hist_line] 32: ***************************************************************************************** 22298434 [M::ha_hist_line] 33: ****************************************************************************************** 22557746 [M::ha_hist_line] 34: ****************************************************************************************** 22440107 [M::ha_hist_line] 35: ***************************************************************************************** 22130525 [M::ha_hist_line] 36: ************************************************************************************** 21459325 [M::ha_hist_line] 37: ********************************************************************************** 20509144 [M::ha_hist_line] 38: ****************************************************************************** 19399337 [M::ha_hist_line] 39: ************************************************************************ 17962454 [M::ha_hist_line] 40: ***************************************************************** 16334878 [M::ha_hist_line] 41: *********************************************************** 14619679 [M::ha_hist_line] 42: *************************************************** 12793736 [M::ha_hist_line] 43: ******************************************** 11035127 [M::ha_hist_line] 44: ************************************** 9361763 [M::ha_hist_line] 45: ******************************* 7757802 [M::ha_hist_line] 46: ************************** 6387930 [M::ha_hist_line] 47: ********************* 5197173 [M::ha_hist_line] 48: ***************** 4122166
2nd histogram
M::ha_hist_line] 1: ****************************************************************************************************> 79362122 [M::ha_hist_line] 2: ****************************************************************************************************> 5824705 [M::ha_hist_line] 3: ****************************************************************************************************> 1842811 [M::ha_hist_line] 4: **************************************************************************************** 934285 [M::ha_hist_line] 5: ************************************************************* 646881 [M::ha_hist_line] 6: ***************************************************** 561993 [M::ha_hist_line] 7: ***************************************************** 563891 [M::ha_hist_line] 8: ********************************************************** 610696 [M::ha_hist_line] 9: **************************************************************** 67923
Third histogram
[M::ha_hist_line] 1: ****************************************************************************************************> 65809002 [M::ha_hist_line] 2: ****************************************************************************************************> 4505333 [M::ha_hist_line] 3: ****************************************************************************************************> 1459641 [M::ha_hist_line] 4: *************************************************************************** 774497 [M::ha_hist_line] 5: ******************************************************* 566043 [M::ha_hist_line] 6: ************************************************* 508811 [M::ha_hist_line] 7: *************************************************** 523826 [M::ha_hist_line] 8: ******************************************************** 572254
Fourth histogram
[M::ha_hist_line] 1: ****************************************************************************************************> 56509704 [M::ha_hist_line] 2: ****************************************************************************************************> 3725834 [M::ha_hist_line] 3: ****************************************************************************************************> 1243762 [M::ha_hist_line] 4: ******************************************************************** 688236 [M::ha_hist_line] 5: **************************************************** 520982 [M::ha_hist_line] 6: *********************************************** 479553 [M::ha_hist_line] 7: ************************************************** 500632 [M::ha_hist_line] 8: ****************************************************** 549716
Fifth histogram
[M::ha_hist_line] 1: ****************************************************************************************************> 50554387 [M::ha_hist_line] 2: ****************************************************************************************************> 3283946 [M::ha_hist_line] 3: ****************************************************************************************************> 1127797 [M::ha_hist_line] 4: **************************************************************** 642271 [M::ha_hist_line] 5: ************************************************** 496973 [M::ha_hist_line] 6: ********************************************** 463586 [M::ha_hist_line] 7: ************************************************* 486543 [M::ha_hist_line] 8: ****************************************************** 534726
The resulting assemlby metrics are low = small split assembly. The coverage given in the gfa files are very low.
With hifi reads the last histogram only has very few kmer seens once left. What parameter could I tweak to improve this?