number of contigs in velvet

[bioenvisage]

hi all , what is the approximate total number of contigs we should get in a velvet assembly? I would like to know this because i did assemblies with various parameters but i always get more then million contigs..

[maasha]

Use VelvetOptimizer.pl

[Zigster]

In a genomic assembly you should get exactly the number of chromosomes for that species or you've made a horrible mistake.

Seriously, i think you are beginning to shoot from the hip with your questions to this board. Post some more specifics or do some research on your own.

[bioinfosm]

What are you trying to assemble?

Here are some numbers from CLCbio tool: http://www.clcbio.com/index.php?id=1413

Lesser, longer contigs are better, provided they are not incorrect!

[bioenvisage]

re

hello zingster ..iam very new to this kind of research and iam not expertise like you in bioinfo ....so only i have these kind of questions araises..im sry if iam hard..

[ECO]

This thread reminds me of something...thanks...(will post the idea in the Site Feedback forum shortly...)

[biomed]

Searching in the dark

Yes, it's better we know the exact chr number. But not all the organisms we know their chromosome. A good way is to align to a closely related organism and then to check the left contigs.

In a genomic assembly you should get exactly the number of chromosomes for that species or you've made a horrible mistake.

Seriously, i think you are beginning to shoot from the hip with your questions to this board. Post some more specifics or do some research on your own.