Hi all, I am puzzled about "-kmer" options during de novo assembly.
First, I did k-mer frequency analysis.
For P(x): Possible peaks including: 100 the unique peak is 100
For F(x): Possible peaks including: 10 103 the unique peak is 103
Raw kmer depth estiamtion:
Curve peak expect_depth
k-mer species 100 100.687
k-mer individuals 103 102.643
Thus I thought the kmer depth of my data is about 101. I thought I should use this value in the following analysis.
Then I began to correct sequencing errors and trim reads containing singleton kmers using bfc. I got advice from a boss. He said I just need to set -kmer value as 61. (my data is 100bp x 2) I once read another paper which set -kmer 61 also. So is it right to just set kmer value as 61? Is there nothing to do with my own data? Why? Thank you.