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Old 10-04-2011, 01:54 AM   #2
boetsie
Senior Member
 
Location: NL, Leiden

Join Date: Feb 2010
Posts: 245
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Hi!

A read is hashed into your defined k-mers. And only ends are considered of the k-mers, simply because you are stripping the read.

Say you have a 10bp read, and a k-mer of 5bp, the hashing of the read into kmers will be;

read: ACGATGATAGTA
kmer: ACGAT
kmer: .CGATG
kmer: ..GATGA
kmer: ...ATGAT
kmer: ....GATAG
kmer: .....ATAGT
kmer: ......TAGTA

The program than finds k-1 overlap (thus here: 5-1=4 bp overlap) at the ends of the k-mers.

E.g:
ACGAT
.CGATG


So you find overlap at the ends of the k-mers, but within the reads.

Have a look at this poster from Velvet for maybe detailed information;

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

Regards,
Boetsie
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