Why does paired end sequencing help assembly?

Dr. Rob Edwards from San Diego State University wonders why paired-end sequencing helps with DNA sequence assembly.

[@khaledpac7797]

Thank you very much Doctor Rob

[@microbialecology41]

I love your videos. Thank you so much for the information.

[@ianmagnus2442]

Your videos are a great resource. I wanted to do a project involving neural networks, sequencing data, and cancer treatment and these videos have been helping immensely.

[@desiderata6997]

a lot of buzz words there hahaha

[@eewls]

Wow, I wish there was more of this

[@luciacolantuono6897]

Thank you!

[@Ammarabd21241]

Thank you

[@stevenhussey461]

1:00 you will only get more than the expected degree of mapping in a region as drawn if it is a repeat that isn't represented in the reference genome but has nonetheless been sequenced

[@julianstanley9516]

Thanks for the video! So I've read that short insert paired-end reads (~up to 800bp) are really easy to ligate adapters to (the A and B adapters that you referenced in the previous video) but that longer reads need to be biotinylated and circularized. Why can't use the same adapter-ligating protocol with long insert paired-end reads as we do with the short insert ones?

[@hafizumar4083]

How does GC content affect assembly?

[@partha_plethorapedia]

Nice explanation sir. What is the difference between PE50 and PE100?

[@GiovanniMotterle]

The title says "paired ends" but you are actually talking about mate pairs.. quite different concepts.

[@sarahansen6597]

mate pairs are often circularized :)

[@GiovanniMotterle]

@@sarahansen6597 to my knowledge mate pairs are always circularized and then can be sequenced through single end or paired end sequencing :)

[@watashiwasho5531]

is it only me that doesn't quite get the answer to the question in the title of this video? :(

[@fridaymorning139]

What does it matter if A goes to B or A goes to D if the two 2000 bp sequences are identical?

[@mathieulemieux8287]

Because in a De Novo sequencing, you can't know in advance that you have a repeated region. You need both region to be correctly placed in the final genome assembly.

[@foodtechnology9457]

Instead of four bases, let's assume that 2 bases are needed for constructing DNA. In this case, how many nodes (excluding the root node) are there in a tree that store all possible 3-mers ?

[@Igormenphito]

Six and bus

[@creatrotera]

this might be stupid, but why not sequence between B and C?

[@soura]

Can someone help me understand why does position of the repeat sequence matters? Is it because one might be inside a coding gene?

[@soura]

Well a year has passed, the position matters because we want to get proper information, doesn't matter it is inside a coding gene or not

[@ozanakar7879]

Thank you so much the same auestion came to my mind 😅

[@Sam-nb1rm]

Still don't know why it's helpful. Thanks anyway

[@cementheed]

Mate-pair, not paired-end - completely different. One is a library strategy, one is a sequencing strategy.