explaining N50 to grand mother

Question

[Prakki Rama]

Hi, If you were asked to explain about genome and its assembly stats like N50 to a naive person, how would you explain and make them understand?

Answer 1

[Lesley Sitter]

I would draw something to explain it.

Telling her that a genome is very large and that is is very hard to find out the 1:1 exact order. Therefore you sequence contigs (or genome fragments or something like that). These fragments are ordered from large to small. You then count up the large fragments until you surpassed the 50% of your total genome size.

Based on the number of fragments you counted and the total amount of fragments you have you can find out how many fragments hold the most information (index). And based on the size of the fragment that passed the 50% mark you can find out if the most information is stored in large or small fragments?

Something like that, idn how much your grandmother knows and why you would even want to explain it to her :P

[lnkgeo58]

I am a grandmother learning about bioinformatics. Let's not assume only the young need to know! ;-)

[Prakki Rama]

Actually I wanted this to know how to explain to a high school student who does not have any knowledge not grand mother. I wanted to make it as simple as possible. Yes. Seems like you need piece of paper and pen to explain it though. Thank you for answer.

[Prakki Rama]

Just thinking, If should explain it in simple sentence. Can I just say, "the point at which is 50% of the genome lies"

Answer 2

[5heikki]

When you have a set of DNA sequences of different lengths and you arrange them from the shortest to the longest, then the N50 value is the length of the shortest sequence that together with all the sequences that are longer than it make up 50% of the sum of total sequence length. As Lesley suggested, you could then draw a simple figure to support learning..

[Lesley Sitter]

The N50 is ordered from longest to shortest and is then the first "long" contig that passes the 50% mark, not the other way around as you mentioned. At least, that is the method used in general papers and even Wikipedia (and we all know that everything on Wikipedia is the absolute truth XD)

[5heikki]

It doesn't matter if you arrange them from the shortest to the longest or the longest to the shortest. Either way you end up with the same exact set of contigs, no?

[Lesley Sitter]

Good point :P but doesn't your index become larger? (there are often more small contigs than large contigs) So if you show it it seems that you have a huge amount of large contigs while in fact your were just looking at it from the wrong side up.

[Prakki Rama]

I think it does not matter how we sort either shortest to longest or vice-versa. But, the adding up the contig size to find the middle point of genome should be done from longest to shortest.