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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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how to adjusting parameters to improve the assembly result #48

Open linshengnan2020 opened 3 years ago

linshengnan2020 commented 3 years ago

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 commented 3 years ago

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

linshengnan2020 commented 3 years ago

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 commented 3 years ago

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