From my understanding if your nodes are too unique then you won't get a very connected graph. I think this blog post is helpful about choosing kmer sizes: homolog.us/blogs/blog/2012/10/10/multi-kmer-de-bruijn-graphs/
You cannot have a k-mer of size larger than the read size because the idea of k-mer is based on dividing the reads into a smaller subset of k-nucleotides so that the complexity of having an undetermined number of reads is eliminated as compared to having a fixed number of k-mers. That being said, having a k-mer of size greater than the read size can cause an increase in the length of contiguous sequence than its actual length in the genome.
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Great explanation. Thanks.
This was really useful, thank you!
Why would you choose a k-mer smaller than your read length? Wouldn't you want a longer k-mer to avoid the problems you were talking about?
From my understanding if your nodes are too unique then you won't get a very connected graph. I think this blog post is helpful about choosing kmer sizes: homolog.us/blogs/blog/2012/10/10/multi-kmer-de-bruijn-graphs/
You cannot have a k-mer of size larger than the read size because the idea of k-mer is based on dividing the reads into a smaller subset of k-nucleotides so that the complexity of having an undetermined number of reads is eliminated as compared to having a fixed number of k-mers. That being said, having a k-mer of size greater than the read size can cause an increase in the length of contiguous sequence than its actual length in the genome.