SEQanswers

Go Back   SEQanswers > Applications Forums > De novo discovery



Similar Threads
Thread Thread Starter Forum Replies Last Post
[Velvet,assembly] core dumped occured by runnning velvet matador3000 De novo discovery 0 12-17-2011 08:31 AM
help on a simple (?) assembly task Kennels Bioinformatics 3 08-08-2011 10:08 PM
Velvet assembly katussa10 De novo discovery 2 12-12-2010 11:22 AM
de novo assembly (velvet or others) strob Bioinformatics 1 01-20-2010 05:53 AM
velvet assembly vani s kulkarni Bioinformatics 25 10-07-2009 12:27 PM

Reply
 
Thread Tools
Old 12-21-2011, 06:19 AM   #1
GBishop
Junior Member
 
Location: New Brunswick, Canada

Join Date: Dec 2011
Posts: 3
Default problem with simple assembly using Velvet

I entered the simple example data that appears on page 9 in Velvet: Algorithms for de novo short read assembly using de Bruijn graphs - link

The file is attached.

I have been unable to get Velvet to assemble the complete sequence.

Could someone let me know what parameters I need to use with velveth and/or velvetg to get the complete 38 bp sequence.
Attached Files
File Type: zip simple1.zip (914 Bytes, 4 views)
GBishop is offline   Reply With Quote
Old 12-22-2011, 06:26 AM   #2
SES
Senior Member
 
Location: Vancouver, BC

Join Date: Mar 2010
Posts: 275
Default

This is not an appropriate example you are trying, it was meant for demonstration purposes only. You would not use Velvet to assemble a 36 bp genome from 7 bp reads. I would recommend reading the manual and downloading some real data from a public site to experiment with. You can see a real world example on slide 16 from that link where a BAC clone is assembled using 35 bp reads with a k-mer length of 31.
SES is offline   Reply With Quote
Old 12-22-2011, 07:51 PM   #3
GBishop
Junior Member
 
Location: New Brunswick, Canada

Join Date: Dec 2011
Posts: 3
Default

Quote:
Originally Posted by SES View Post
This is not an appropriate example you are trying, it was meant for demonstration purposes only. You would not use Velvet to assemble a 36 bp genome from 7 bp reads. I would recommend reading the manual and downloading some real data from a public site to experiment with. You can see a real world example on slide 16 from that link where a BAC clone is assembled using 35 bp reads with a k-mer length of 31.
Thanks for the reply. The author of the paper does state on slide 13 "Velvet is able to resolve this toy example". Being a beginner in the de novo assembly world, I was hoping someone would be able to repeat what the author stated he could do with Velvet.
GBishop is offline   Reply With Quote
Old 12-23-2011, 07:28 AM   #4
SES
Senior Member
 
Location: Vancouver, BC

Join Date: Mar 2010
Posts: 275
Default

Quote:
Originally Posted by GBishop View Post
Thanks for the reply. The author of the paper does state on slide 13 "Velvet is able to resolve this toy example". Being a beginner in the de novo assembly world, I was hoping someone would be able to repeat what the author stated he could do with Velvet.
Did you run velveth with the same parameters (k=5)? I was going to provide links to real datasets but I think it may be more helpful for you to read the manual.

Also, you will find it more productive for yourself and everyone that reads this in the future to spend a little time searching the internet and thoroughly reading any documentation and publications you can find about the topic. That way you can ask a more specific question and others can spend less time trying to figure out what you are asking.
SES is offline   Reply With Quote
Old 12-23-2011, 06:49 PM   #5
GBishop
Junior Member
 
Location: New Brunswick, Canada

Join Date: Dec 2011
Posts: 3
Default

Quote:
Originally Posted by SES View Post
Did you run velveth with the same parameters (k=5)? I was going to provide links to real datasets but I think it may be more helpful for you to read the manual.

Also, you will find it more productive for yourself and everyone that reads this in the future to spend a little time searching the internet and thoroughly reading any documentation and publications you can find about the topic. That way you can ask a more specific question and others can spend less time trying to figure out what you are asking.
Yes, I ran velveth with k=5. I did read the manual that came with the velvet software and have spend time searching the Internet to learn about de novo software for SOLiD data.

It's unlikely I would have taken the time to enter the data and try this simple analysis if the author hadn't stated that velvet was able to sequence it.
GBishop is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:24 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO