Velvet lengyh k-mers

[sinnamone]

Hi at all,
i have a question, i'm using velvet for de nove assembly. Why when i put length k-mers= 22, 24, 26,28, 30, I have this message = velvet can't work with even length k-mers. We'll use xx instead.

[ctseto]

Working as intended.

5.2 Choice of hash length k
The hash length is the length of the k-mers being entered in the hash table.
Firstly, you must observe three technical constraints:
• it must be an odd number, to avoid palindromes. If you put in an even
number, Velvet will just decrement it and proceed.

http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf

And from Zerbino's original paper:

To ensure that each k-mer cannot be its own reverse complement, k must be odd.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336801/

In short, velvet is not intended to use even-numbered Kmers. It will decrement to 21, 23, 25, 27,29.
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My limited understanding of the palindromic condition follows, with a theoretical example:

For example, a region of:

5-ATGCATGCATGCATGC-3
3-TACGTACGTACGTACG-5

With a K of 2: AT, is its own forward and reverse complement (and GC's reverse complement is GC as well, and CG's reverse complement is CG, but not AG (which is CT).)

ATG's reverse complement is CAT. ATGC's reverse complement is GCAT, which presents a non-palindromic reverse complement. At the end of the day the palindromes depend on a highly repetitive pattern /and/ an even Kmer. Not all even Kmers are palindromic, but an even-Kmer is required to set up a palindromic condition.