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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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Parameters to change for high heterozygosity #66

Closed lstevens17 closed 5 years ago

lstevens17 commented 5 years ago

Hello,

One of my ONT datasets is from a very heterozygous nematode genome. Ideally, I'd like to end up with a haploid assembly. With Canu, you typically achieve this by increasing the corrected error rate parameter to allow for a larger number of differences between reads/overlaps.

Do you have any suggestions for which parameters within wtdbg2 to change/play with in order to collapse heterozygosity? The default parameters in wtdbg2 yield an assembly with a larger than expected span, suggesting haplotypes are being separated.

Thanks for your help,

Lewis

ruanjue commented 5 years ago

Usually, wtdbg2 collapses heterozygosity. In your case, please try to decrease -k/-p and use -S 2 to find more overlaps between less identity sequences. It will comsume more RAM and take more time.

Best, Jue

lstevens17 commented 5 years ago

Thanks for this - will give it a go!

Lewis