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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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Haploid genome assembly - weird k-mer distribution #139

Closed vsuryaw closed 5 years ago

vsuryaw commented 5 years ago

Screen Shot 2019-08-14 at 1 08 33 AM

Hi,

We have 100x reads from PacBio Sequel for a gametophyte genome (approx size 500Mb) and is essentially a haploid genome. Upon running wtdbg2 with default settings, we get the k-mer distribution attached.

What would be your advice on tuning the parameters for this assembly? Also as an aside, 100% of the reads were clipped when a student ran this and he got no output result.

ruanjue commented 5 years ago

Have a try with -x preset3 to increase the k-mer size.

vsuryaw commented 5 years ago

Thanks, we got it solved.