how to adjusting parameters to improve the assembly result

[linshengnan2020]

hi, I have run a 1G , diploid genome with 70~80% repetitive sequences genome . The coverage of my PacBio data is approximately 40 x. As a result the final assembly N50 is 82k . I would be interested how to adjust the parameters to improve the assembly result. Could you please give me some advises? Thank you very much!

[ruanjue]

Try other assemblers first, if all give small N50, let us discuss it again.

[linshengnan2020]

I have used several assemblers ，such as mecat2, flye, WTDBG2, smartdenovo and nextdenovo , the results of smartdenovo and nextdenovo were relatively good, the N50 is 82k and 157k.

[ruanjue]

Have a look at smartdenovo.pl, have you chosen the zmo engine? The default is dmo, much faster, but gives reletively worse alignments.