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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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Kmer selection #21

Closed njaupan closed 6 years ago

njaupan commented 6 years ago

Dear Ruanjue,

If I understand correctly, smartdenovo works very different from DBG assemblers, is kind of OLC assembler. So i am not sure if kmer selection should be done based on Jelleyfish or Kmergenie. Therefore, how to select kmer size for smartdenovo?

Sincrely, panpan

ruanjue commented 6 years ago

K-mer is used in SMARTdenovo for reads aligning. The default setting is ok in most case. For more details, please have a look at https://github.com/ruanjue/smartdenovo/blob/master/README-tools.md .