Question: what is the benefit of the de bruijn algorithm for short read assembly?
3
gravatar for seta
3.6 years ago by
seta1.3k
Sweden
seta1.3k wrote:

Hi all,

First of sorry if the question is a basic for you. Could you please explain to me why the short reads are broken into shorter fragments (K-mer) and then found the overlap k-mer by the de Bruijn algorithm-based assembler software for transcriptome assembly, instead of using the entire read for finding the overlap segments? Please let me kindly know what is the benefit of such algorithms in relative to overlap algorithm used by CAP3?

Thanks

ADD COMMENTlink written 3.6 years ago by seta1.3k
1

Time... It takes a lot more time to do it the old fashion way (with overlap), every read has to be checked with every other read.

ADD REPLYlink written 3.6 years ago by Benn8.0k
1

If you like tutorials in-addition to papers Homolog-blog covers really cool things about denovo assembly in general. Take a look :)

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Rohit1.4k

This is a slightly older paper but in case you have not seen it, it would be useful.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by genomax83k

You might file following papers useful.

Comparison of De Novo Genome Assembly Software

Sequence assembly demystified

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Sej Modha4.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1674 users visited in the last hour