Is there any relation between DNA integrity and contigs size?

[soleulloa]

Hi all,

I need to know if DNA integrity has any relation with contigs size?
For example, if my DNA is more degraded I should obtain littlest contigs?

Thanks
Soledad

[pmiguel]

Glossing over some details:
As long as the majority of your DNA is more than 5X longer than the average insert size of your library amplicons, then no there would be no relation between DNA integrity and contig sizes.

That is, you are going to fragment the DNA prior to creating your library anyway.

But, if you are making large "insert" mate pair libraries degredation of your input DNA could be an issue.

All of this presumes your DNA is now free of DNAses -- which is questionable given that it became degraded somehow.

It also presumes that the process degrading your DNA is relatively random. If your DNA were subject to a complete EcoRI digestion prior to library construction, then the resulting sequence data would probably be incapable of spanning any EcoRI sites.

Likely the biggest problem with degraded DNA is that if it has one problem (high levels of strand cleavage) it may well have other problems not so obvious from running a gel...

--
Phillip

[wdecoster]

In addition to what pmiguel said, when using technologies such as PacBio and Oxford Nanopore the DNA integrity is very important because longer reads will help bridge repetitive elements and generate as such longer contigs.

[nucacidhunter]

I should add 10x Genomics libraries which prepares linked-reads for long range genomic information using Illumina’s short reads. The quality of data for de novo assembly or phasing applications is heavily dependent on DNA integrity although the platform does not use long reads such as PacBio or Nanopore.

[soleulloa]

Thanks all.
My question is relative about "bad quality assembly".
How many contigs less than 1000 bp do you expect in a MiSeq 300 cycles run? How much of those are ok?
I am trying to link that paramether with DNA integrity (thinking in very short fragments after transposase).

What do you think could be a reason to get littlest contigs?
Maybe is a complex genome issue? (%GC, repetitive regions)
Regards!
Soledad

[nucacidhunter]

In this case:
1- coverage
2- library diversity
3- repetitive region
4- GC content if over 70%
5- ploidy and heterozygosity
6- assembly software

[GenoMax]

@soleulloa: What is the expected genome size?