NGS Applications¶

Lecture Notes¶

Challenges¶

In our challenge we are looking for gene(s)/biotic factor(s) that are responsible for fluffiness in a hypothetical species. Find below some information about the species if necessary make further assumptions. There is no need to have a perfect solution. The main idea of the challenges is to discuss your own ideas critically in your group. Post your ideas directly in the Google group.

Aim: Looking for the fluffy gene(s)/botic factors

Information about the species:

Two distinct phenotype found in nature (fluffy and smooth) 
Fluffy phenotype is rare  
Mechanism unknown (genetic and/or biotic factors)
Large and uncharacterised (1 Gb) genome
3 years project
Small budget

(1) Which applications/methods do you use and why? (Hint: Genomic, Transcriptomic or Amplicon/Metagenomic approach)

(2) Which sequencing platform do you use and why?

(3) What sampling design do you use?

(4) How many units/lanes/bells you need to run? (Hint: Assume a reasonable coverage and use the coverage calculator)

(5) Is there a way to validate your candidate gene(s)/biotic factors?

Additional Information¶

Applications of next-generation sequencing

Coverage Calculator¶

Illumina
Neb