K-mers

[charltt]

Hey all,

I am an undergrad who is just getting into bioinformatics and I am looking to understand a little bit more about NGS and assembly technology. In my reading, I am consistently finding discussion about k-mer length but I am yet to find a really good explanation of what exactly a k-mer is. Can anyone help me out, or point me in the direction of a good source to help me understand this a little better?

Thanks!

[Richard Finney]

http://en.wikipedia.org/wiki/K-mer

[grassgirl]

k-mers are 'words of k nucleotides' where k is the length of the string of nucleotides and is variable. The k-mers are used to compare against reads in assembly algorithms such as Velvet. When these algorithms are run, the user can specify the k-mer size, within reason. Here is a link to a paper describing it in detail with regards to how Velvet works:

http://genome.cshlp.org/content/18/5/821.full