Genome Sequencing and Assembly: A Comprehensive Guide for Biotechnology Students

Question 1

Which of the following is not a commonly used next-generation sequencing (NGS) platform?

Accepted Answer

Capillary electrophoresis

Answer

Illumina

Answer

Ion Torrent

Answer

Pacific Biosciences

Question 2

Which assembly algorithm is best suited for assembling long, high-quality reads?

Accepted Answer

Overlap-Layout-Consensus (OLC) assembly

Answer

De Bruijn graph assembly

Answer

Hierarchical assembly

Answer

Reference-guided assembly

Question 3

What is the primary function of a de Bruijn graph in genome assembly?

Accepted Answer

To represent overlaps between reads

Answer

To identify and remove sequencing errors

Answer

To assemble contigs from overlapping reads

Answer

To align reads to a reference genome

Question 4

What sample preparation technique is essential for producing high-quality genome sequencing data from many samples?

Accepted Answer

DNA fragmentation and library preparation

Answer

Long-read sequencing

Answer

PCR amplification

Answer

RNA isolation

Question 5

What metric is typically used to assess the quality of a genome assembly?

Accepted Answer

N50

Answer

GC content

Answer

Read depth

Answer

Coverage

Question 6

Which of the following algorithms is commonly used for short-read genome assembly and is based on the construction of a de Bruijn graph?

Accepted Answer

De Bruijn graph assembly

Answer

Overlap-layout-consensus assembly

Answer

Hierarchical assembly

Answer

Single-molecule sequencing assembly

Question 7

Which of the following is NOT a potential application of genome sequencing in biotechnology?

Accepted Answer

Prediction of weather patterns

Answer

Disease diagnosis and prognosis

Answer

Personalized medicine and treatment

Answer

Genetic engineering and crop improvement

Question 8

Which step in the Sanger sequencing method involves annealing primers to single-stranded DNA?

Accepted Answer

Annealing

Answer

Denaturing

Answer

Elongation

Answer

Termination

Question 9

What is the primary objective of genome assembly?

Accepted Answer

To determine the order and orientation of DNA fragments

Answer

To align all sequenced reads into a single consensus sequence

Answer

To identify and correct sequencing errors

Answer

To annotate genes and other genomic features

Question 10

Which assembly algorithm constructs a de Bruijn graph to reconstruct contigs?

Accepted Answer

Eulerian Path

Answer

Overlap-Layout-Consensus

Answer

Greedy

Answer

Hierarchical

Question 11

What does the N50 value represent in the context of genome assembly?

Accepted Answer

The length at which 50% of the assembly is contained

Answer

The length of the longest contig

Answer

The number of contigs in the assembly

Answer

The number of gaps in the assembly

Question 12

What is the purpose of a reference genome?

Accepted Answer

To provide a complete and annotated genome sequence for comparison

Answer

To identify all genes present in an organism

Answer

To create a model for predicting genetic variations

Answer

To store genetic data from multiple individuals

Question 13

Which of the following is a next-generation sequencing (NGS) technology used for high-throughput DNA sequencing?

Accepted Answer

Illumina HiSeq

Answer

Sanger sequencing

Answer

Microarray

Answer

Karyotyping

Question 14

In genome assembly, what is the primary function of a reference genome?

Accepted Answer

Provides a scaffold to align reads during assembly

Answer

Acts as a control for quality assessment

Answer

Contains a database for gene annotation

Answer

Serves as a target sequence for primer design

Question 15

What is the primary type of error that can occur during sequencing?

Accepted Answer

Base substitution

Answer

Gene duplication

Answer

Chromosome translocation

Answer

Point mutation

Question 16

What is the main purpose of quality assessment in genome sequencing?

Accepted Answer

Identifies and eliminates low-quality reads

Answer

Predicts the gene content

Answer

Determines the length of the assembled genome

Answer

Helps design primers for PCR amplification

Question 17

What is the key advantage of using long reads for genome assembly?

Accepted Answer

Ability to span larger genomic regions

Answer

Easier to align

Answer

Higher accuracy

Answer

Lower cost

Question 18

Which of the following bioinformatics tools is primarily used for genome annotation?

Accepted Answer

Geneious

Answer

Adobe Photoshop

Answer

Excel

Answer

Microsoft Word

Question 19

What is a major ethical concern associated with genome sequencing?

Accepted Answer

Privacy implications

Answer

Cost of sequencing

Answer

Time required for sequencing

Question 20

What is a predicted trend regarding the future of genome sequencing?

Accepted Answer

Decreased cost and increased accessibility

Answer

Discontinuation due to ethical concerns

Answer

Exclusive use for research purposes

Answer

Uncertain due to lack of innovation

Question 21

Which of the following sequencing technologies is NOT considered a next-generation sequencing (NGS) method?

Accepted Answer

Sanger sequencing

Answer

PacBio sequencing

Answer

Illumina sequencing

Answer

Nanopore sequencing

Question 22

What is the primary purpose of quality assessment in genome sequencing and assembly?

Accepted Answer

To identify and correct errors in the sequencing data

Answer

To determine the length of the genome

Answer

To identify genes and other functional elements

Question 23

Which of the following is a significant advantage of using paired-end sequencing in genome assembly?

Accepted Answer

Improved ability to resolve repetitive regions and create longer, more accurate contigs

Answer

Reduced sequencing cost

Answer

Ability to sequence larger genomes

Answer

Increased speed of sequencing

Question 24

What is the primary function of a reference genome in the process of genome assembly?

Accepted Answer

To serve as a guide for aligning and assembling sequencing reads into a contiguous genome sequence

Answer

To determine the genetic diversity of a population

Answer

To identify and correct errors in the sequencing data

Question 25

What is the main purpose of scaffolding in genome assembly?

Accepted Answer

To link together contigs into larger, more complete scaffolds, improving the overall assembly quality

Answer

To determine the orientation of contigs

Answer

To identify gaps in the assembly

Answer

To identify and correct errors in the sequencing data

Question 26

What is the ultimate objective of genome sequencing and assembly?

Accepted Answer

To produce a complete and accurate representation of an organism's entire genome sequence

Answer

To identify disease-causing mutations

Answer

To study gene expression

Question 27

Which of the following fields is a significant application of genome sequencing and assembly in medicine?

Accepted Answer

Personalized medicine, allowing for tailored treatment based on an individual's genetic makeup

Answer

Conservation biology

Answer

Forensic science

Answer

Agriculture