The real problem with Whole Genome Sequencing (WGS)

Genome Assembly from Raw Read Data from short-reads

I am going to do two experiments:

{Exp. 1} First I will assume that I have a valid Reference Genome. Then I will create different In Silico Library preparations that do not contain the Target Genome (From Completely Random, to consistent with biological samples related to the Target Genome). Finally I will compute the probability of recreating the Reference Genome via Bioinformatics Techniques, even though, it should not be there.

{Exp. 2} The second part of the experiment is more complex and involves de Novo sequencing. How broad is the variability within the consensus sequence?

Objectives:

{From Exp.1} Can I sequence something that is not there at all? What is the error range?

{From Exp.2, The Most Important Question} Can I create In Silico Chimeras that do not exist in reality at all, by putting together different pieces of things (i.e. ORF, N, E, S…) that actually do exist in reality in many different organism, and obtain a consistent positive reading of things that do not exist in reality, from samples taken within the target ecosystem of my study (i.e. The Human Body)?

Scheme of The Problem:

(Source of the Picture)

NOTE: The experiment may take some time. I’ve worked in Bioinformatics before, however there are many techniques that I have to learn in order to do this, there will be problems that I cannot predict and I have to familiarized myself with different types of software.

Why the need to analyze this? Some perspective:

My current thesis is in very much agreement with Dr. Wolfgang Wodarg. You can hear him here in conversation with Dr. Paul E. Marik:

I’ve been thinking in this direction from the very beginning. In my opinion it doesn’t contradicts what Dr. Paul E. Marik is saying. One thing is the evolving genome sequence that we are measuring all over the planet, the so called SARS-CoV-2, and another very distinct thing is the clinical presentation called COVID-19 (more precisely, Severe COVID), which causation may or may not be SARS-CoV-2.

As Dr. Paul. E. Marik said “I didn't put much credence in the PCR, because it's a clinical diagnosis, once the patients come to the ICU and you get a chest X-ray and a CAT scan, you then get a ferritin, a COP and lymphocytes count, there's no other diagnosis.”

(Source) The whole debate can be found here at the end of the presentation by Dr. Paul E. Marik https://odysee.com/@Corona-Investigative-Committee:5/Session-109-Marik-Odysee-final:6

The debate with Dr. Wolfgang Wodarg starts at:

See you in the Future!

Take Care,

Agus