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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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p(kmer) VS k(kmer) Question(s) #216

Open cement-head opened 4 years ago

cement-head commented 4 years ago

Hi Jue and Heng,

Would be able to answer this question: https://bioinformatics.stackexchange.com/questions/7029/wtdbg2-practical-implications-of-k-mer-fsize-and-psize-choice

Thanks!

ruanjue commented 4 years ago

On sensitivity, kmer-psize is better. On specificity, kmer-fsize is better. It is allowed to use -k 2 -p 19 to get a bit more specificity b ut less sensitivity than -p 21 in wtdbg.