scaffold N50 is the median contig size of your genomic assembly. It's a metric that you can use to evaluate the quality of your assembly, since an overly small N50 suggests that you were unable to generate many contigs of biologically meaningful size (i.e. you probably have a lot of bogus little contigs in your assembly). You can increase your N50 by eliminating sequences which are bound to cause you problems, e.g. short repetitive stretches.

note that this metric only applies when doing de novo assembly. If you are aligning to a reference (i.e. for variant discovery applications) this metric doesn't apply

Thank you Dan Spiegelman,

It is good and more explainery information for me to understand the information.

I ahve another question related to ur topic realted to reference assembly, actualy i need some good tool for doing reference assemsbly.

Currently have gone throught some tools, but got simple software CLC Workbench as a good tool for the same.

but it is commercial and also have the limitation regarding the memory size for my assembly, so can you suggest some tool for the same.

Thanking you again,

Vishal Mevada

Vishal,

There is a free resource for next-generation sequencing information called: SEQanswers.com

The thread relevant to your question regarding the definition of N50 is at:

http://seqanswers.com/forums/showthread.php?t=2332&highlight=N50+definition

Good Luck!

-Kevin

Vishal,

There are many software/tools for doing reference based genome assembly. Probably it depends on the platform you are using for sequencing.

If you are using SOLiD , then you can use bioscope or lifescope which comes with the SOLiD software itself. there are many others too like tophat, bowtie cufflink and may more. you have to choose depending on the platform.

Hope it helps

Neha

If you are looking for measuring performance of genome assembler , you may use http://crdd.osdd.net/raghava/genomeabc/

You can find a very good explanation here: https://www.molecularecologist.com/2017/03/29/whats-n50/