Query on K-mer using in velvet

ramadatta.88 · 10-03-2011, 11:43 PM

Hi, I am newbie to NGS. TO assemble a genome i started using velvet. During which I came across a term called 'K-mer' which means the overlapping segment in the reads. I would like to know that if the K-mer length assigned is suppose 21, is it that the overlapping is done exactly for 21 nucleotides at the ends or is it a minimum requirement for the reads to match? Could i kindly know the difference..Thanks in advance..

boetsie · 10-04-2011, 01:54 AM

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

ramadatta.88 · 10-04-2011, 08:23 PM

thank you..My doubt is cleared..

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10-03-2011, 11:43 PM	#1
ramadatta.88 Junior Member Location: singapore Join Date: Sep 2011 Posts: 7	Query on K-mer using in velvet Hi, I am newbie to NGS. TO assemble a genome i started using velvet. During which I came across a term called 'K-mer' which means the overlapping segment in the reads. I would like to know that if the K-mer length assigned is suppose 21, is it that the overlapping is done exactly for 21 nucleotides at the ends or is it a minimum requirement for the reads to match? Could i kindly know the difference..Thanks in advance..

10-04-2011, 01:54 AM	#2
boetsie Senior Member Location: NL, Leiden Join Date: Feb 2010 Posts: 245	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

10-04-2011, 08:23 PM	#3
ramadatta.88 Junior Member Location: singapore Join Date: Sep 2011 Posts: 7	thank you..My doubt is cleared..