good assemblies with low kmer coverage

ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

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good assemblies with low kmer coverage #69

Closed MichelMoser closed 5 years ago

MichelMoser commented 5 years ago

Hi,

When experimenting with different coverage cutoffs of nanopore data, i seem to be getting best assemblies with very low average kmer coverage (5 x) and very right-skewed kmer histograms.

Is there an explanation for this?

Also i see a drop in assembly N50 when adding more data then 20x of ONT data but almost no change in total assembly size.

Is more data just confusing the fuzzy Bruijn graph?

Thanks, Michel

ruanjue commented 5 years ago

There was a line in log message, like KEY PARAMETERS: .... Please check whether it differed among your tests. If it still is confused, please send me the log files to me ruanjue(AT)gmail.com, thanks!

Jue