De bruijn graphs

[anil KR]

Hi,

Can anyone explain about the de Bruijn graph algorithms like how does it constructs the contigs from short read sequences? What i understood is that it constructs contigs basing on number of times the short reads ending with A,G,T,C . For instance , if a short read ending with A nucleotides are higher than the other short reads then it joins to the existing short read. This is how it constructs the contigs? Does ,this explaination is correct?

Thanks in Advance!

Anil.

[mastal]

De bruijn graphs

Have a look at the velvet webpage

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

Follow the links to the 2 velvet publications, they will explain how velvet works.

[maasha]

The CLC explanation is nice and crisp:

http://www.clcsupport.com/clcassemblycell/current/index.php?manual=How_it_works.html

[anil KR]

Hi mastal,

I have looked the paper previously but i didn't understand how the algorithms are working?


Anil.

[anil KR]

Hi,


Thanks to mastal and maasha for the links. i am looking into it and seems it would be helpful for understanding the graphs.

Anil.

[GenoMax]

Nature biotechnology has a good article: http://www.nature.com/nbt/journal/v2.../nbt.2023.html

If you do not have access to an online subscription then here is the reference : Nature Biotechnology, Vol 29, 987–991 (2011)

[syfo]

Nature biotechnology has a good article: http://www.nature.com/nbt/journal/v2.../nbt.2023.html

If you do not have access to an online subscription then here is the reference : Nature Biotechnology, Vol 29, 987–991 (2011)

This great article is available in open access here (pdf)

[kadircaner]

I think following is one of the best tutorials I've seen so far:

http://www.homolog.us/Tutorials/index.php?p=1.1&s=1

[anil KR]

Thanks to Genomax,syfo and kadircaner the stuff is really useful.


Thanks alot!

Anil.