1/ HI Ben, It has been a while since your first post on assembly, and my comments there. At that time I did not yet read the Wu paper, nor did know the details of the assembly program Megahit. I imagined how an assembly program might work and imagined that it would take a very long time to run the program. I see that Megahit extracts "K-…
1/ HI Ben, It has been a while since your first post on assembly, and my comments there. At that time I did not yet read the Wu paper, nor did know the details of the assembly program Megahit. I imagined how an assembly program might work and imagined that it would take a very long time to run the program. I see that Megahit extracts "K-mers" of odd length (eg 27nt). A 27nt segment of the viral genome would be covered by many reads, but in the ideal world, the very same k-mer would be extracted from many reads, reducing redundancy, and making the program fast.
1/ HI Ben, It has been a while since your first post on assembly, and my comments there. At that time I did not yet read the Wu paper, nor did know the details of the assembly program Megahit. I imagined how an assembly program might work and imagined that it would take a very long time to run the program. I see that Megahit extracts "K-mers" of odd length (eg 27nt). A 27nt segment of the viral genome would be covered by many reads, but in the ideal world, the very same k-mer would be extracted from many reads, reducing redundancy, and making the program fast.