Explaining My Project
From GcatWiki
Shotgun Sequencing
Counting Kmers to Tell you about Genome
(taken from https://banana-slug.soe.ucsc.edu/bioinformatic_tools:jellyfish)
- Bad kmer rate = bad multiplicity kmers/total number of all kmers
- Seq Error Rate = bad kmer Rate/kmer size
- Genome Coverage = use gamma fit on the good multiplicity values of the best kmer (usually largest). The peak of this line gives genome coverage (see red line) (here about 47.11x)
- Genome size = number of unique good multiplicity kmers/coverage
- 1st peak (@ low multiplicity) = from seq errors
- 2nd peak = multiple copies of the same location in the genome
- If a k-mer occurs n times in the genome, we would expect to see it n times as often in the sequencing, so there should be additional peaks for k-mers that occur in repeats.
