problem with simple assembly using Velvet

[GBishop]

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.

[SES]

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.

[GBishop]

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.

[SES]

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.

[GBishop]

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.