Hi
I am doing de novo assembly of a bacterial genome, through paired end reads using velvet.
If I use Kmer length 75, in the Kmer coverage formula along with other parameters I get:
Ck = C * (L - k + 1) / L
Ck=(2935775*250*2/2900000) *(250-75+1)/250
=356
where length of reads in 250
Number of reads:2935775
expected genome size is 2900000
Velvet manual says : If Ck is above 20, you might be "wasting" coverage. What does it mean and what Kmer should I choose?
I am doing de novo assembly of a bacterial genome, through paired end reads using velvet.
If I use Kmer length 75, in the Kmer coverage formula along with other parameters I get:
Ck = C * (L - k + 1) / L
Ck=(2935775*250*2/2900000) *(250-75+1)/250
=356
where length of reads in 250
Number of reads:2935775
expected genome size is 2900000
Velvet manual says : If Ck is above 20, you might be "wasting" coverage. What does it mean and what Kmer should I choose?
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