Reference no: EM132990346

Question 1 

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

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

Question 2

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

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

Question 3

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

Question 4

What factors make NGS faster and cheaper than Sanger sequencing?

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

Question 5

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

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

Question 6

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

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.

Question 7

Which best describes "resequencing"?

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

Question 8

Which best describes "de novo assembly"?

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

Question 9

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.

Question 10

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.))?