De bruijn graphs

anil KR · 06-24-2013, 03:29 AM

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 · 06-24-2013, 03:51 AM

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 · 06-24-2013, 03:54 AM

The CLC explanation is nice and crisp:

http://www.clcsupport.com/clcassembl..._it_works.html

anil KR · 06-24-2013, 03:58 AM

Hi mastal,

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

Anil.

anil KR · 06-24-2013, 04:05 AM

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 · 06-24-2013, 04:20 AM

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 · 06-24-2013, 08:02 AM

Quote:

Originally Posted by 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)

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

kadircaner · 06-24-2013, 08:49 AM

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 · 06-25-2013, 12:33 AM

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

Thanks alot!

Anil.

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06-24-2013, 03:29 AM	#1
anil KR Junior Member Location: norway Join Date: Jan 2013 Posts: 8	De bruijn graphs 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. Last edited by anil KR; 06-24-2013 at 03:41 AM.

06-24-2013, 03:51 AM	#2
mastal Senior Member Location: uk Join Date: Mar 2009 Posts: 667	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.

06-24-2013, 04:20 AM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,082	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) Last edited by GenoMax; 06-28-2013 at 12:00 PM. Reason: Corrected link

06-24-2013, 03:54 AM	#3
maasha Senior Member Location: Denmark Join Date: Apr 2009 Posts: 153	The CLC explanation is nice and crisp: http://www.clcsupport.com/clcassembl..._it_works.html

06-24-2013, 03:58 AM	#4
anil KR Junior Member Location: norway Join Date: Jan 2013 Posts: 8	Hi mastal, I have looked the paper previously but i didn't understand how the algorithms are working? Anil.

06-24-2013, 04:05 AM	#5
anil KR Junior Member Location: norway Join Date: Jan 2013 Posts: 8	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.

06-24-2013, 08:49 AM	#8
kadircaner Member Location: Houston,TX Join Date: Jun 2011 Posts: 13	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

06-25-2013, 12:33 AM	#9
anil KR Junior Member Location: norway Join Date: Jan 2013 Posts: 8	Thanks to Genomax,syfo and kadircaner the stuff is really useful. Thanks alot! Anil.