QUIZ!#

Class 4 quiz

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Flag question: Question 1

Question 1 1 pts

Compared to so-called "Next-generation" or "Massively parallele" sequencing, what would be "First generation" sequencing?

Group of answer choices

a. Gel and/or capillary electrophoresis (CE) readout

b. PCR based sequencing methods of sequencing

c. Sanger, dideoxy chain-termination sequencing

d. Single molecule sequencing, for example with nanopores

 

Flag question: Question 2

Question 2 1 pts

What are key advantages of NGS compared to "First-generation" sequencing?

Group of answer choices

a. Reduced need for input sample (i.e. clone libraries)

b. Reduced need for size separation steps

c. Parallel readouts

d. All of the above

 

Flag question: Question 3

Question 3 1 pts

How do read lengths compare for Sanger vs NGS? This is a generalization, as newer technologies are improving things all the time

Group of answer choices

a. Sanger reads are usually shorter than NGS reads but the contigs are longer

b. Sanger reads are usually about the same as NGS reads

c. Sanger reads are usually longer than the most commonly encountered NGS reads

d. Sanger reads are rarely if ever longer than NGS, though the error profile is better

 

Flag question: Question 4

Question 4 1 pts

What factors make NGS faster and cheaper than Sanger sequencing?

Group of answer choices

a. Accuracy improvements streamline downstream processing

b. Shorter read lengths save time and money during sequencing and bioinformatics processing

c. Highly parallelized, smaller volumes, less input sample required

d. None of the above

 

Flag question: Question 5

Question 5 1 pts

Why are short reads problematic for some sequencing applications? This is a generalization, and "short" may be relative.

Group of answer choices

a. Short reads may be ambiguous with regard to overlap or genomic placement (i.e. "mapping").

b. Short reads impact de novo assembly but not genotyping or sequencing per se

c. Short reads impact genotyping but not assembly or sequencing per se

d. Short reads primarily just increase error rates and therefore costs

 

Flag question: Question 6

Question 6 1 pts

Which best describes "mate-pairs" or "paired-end" reads

Group of answer choices

a. Shorter reads paired together to increase the total read length of your reaction.

b. Two reads separated by approximately known distance on a single starting DNA molecule.

c. Two reads taken together from the same sample DNA and arranged so as to span gaps.

d. Paired reads that align to form contigs then scaffolds, i.e. for genome assembly.

 

Flag question: Question 7

Question 7 1 pts

Which best describes "resequencing"?

Group of answer choices

a. Alignment of reads from one sample relative to a reference to identify variants.

b. Overlap of reads into contigs then scaffolds then an assembly.

c. Alignment of reads to find sequence features associated with phenotypes.

d. All of the above

 

Flag question: Question 8

Question 8 1 pts

Which best describes "de novo assembly"?

Group of answer choices

a. Alignment of reads from one sample relative to a reference to identify variants.

b. Overlap of reads into contigs then scaffolds then an assembly.

c. Alignment of reads to find sequence features associated with phenotypes.

d. All of the above

 

Flag question: Question 9

Question 9 3 pts

How does too-short read length impact common genomics applications? Specifically, how do short reads impact SNP genotyping and discovery? How do short reads impact assembly? Note "short" is a relevant term, but "too-short" implies functional limitations.

 

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Flag question: Question 10

Question 10 3 pts

How would you summarize the approach to sequencing advocated in the assigned paper (Aury JM, et. al. (2008) BMC Genomics, 9: 603. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies (Links to an external site.) )?

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