30 Questions
What is the purpose of a barcode in Illumina sequencing?
Enables simultaneous sequencing of multiple samples
What is the function of adapters in Illumina workflow?
Known primers added to ends of DNA fragments
What does a flow cell in Illumina sequencing consist of?
Glass slide with oligos that attach to adapters
What is the role of cluster in Illumina sequencing?
Formed after bridge amplification, multiple copies of the same DNA strand on flow cell
What does base calling from raw data involve in Illumina sequencing?
Interpreting the identity of the base from the color of a cluster
What is the format of FASTQ files in Illumina sequencing?
A txt file with four lines per read
What is the significance of quality values in Illumina sequencing?
Represent the certainty of the base determined by the clarity of the spot on the flow cell
What is the term for the rapid increase in frequency of a specific genetic variant due to positive natural selection?
Selective sweep
Which of the following is a measure of the amount of genetic variation in a population?
Heterozygosity
Which enzyme shears DNA at specific sites?
ApeKI
Which allele is related to metabolism in bobcats, affecting energy expenditure and obesity?
GPR158
Which allele is related to abdominal fat storage and lipid metabolism in bobcats?
LECT2
Which allele is related to noxious heat detection in bobcats?
TRPM
What is the term for distinct chromosomal regions where genetic variants are inherited together?
Linkage disequilibrium
What does Fst measure in population genetics?
Divergence between populations
What is the term for the process of identifying structural rearrangements in the genome?
CNVs
What is the best Phred quality score indicating high consistency in DNA sequencing?
30
Which method is suitable for de novo bacterial/viral genome assembly and BAC sequencing?
Pac bio (NGS)
What does copy number variation (CNV) refer to?
Variation in repeated genome sequences
What do string graphs in de novo assembly use to construct full sequence contigs?
Nodes representing reads
What is the focus of transcriptome analysis?
RNA molecules in cells
What is the method for SNP detection in genomes and can be used in genetic mapping and estimation of allele frequencies?
RADseq
How are consensus sequences obtained from de novo assembly contigs based on?
Weighted voting, incorporating quality scores for accuracy
What is the main purpose of genome re-sequencing?
To gather data on genetic variation through mapping reads to a known reference sequence
What is the calculation of N50 for a given genome assembly with contig lengths of 5mb, 25mb, 40mb, and 30mb?
30mb
What is the purpose of large scaffolds in genomes with many repeats?
To be generated using mate pair libraries and methods that produce very long reads
What are the cost-saving approaches for genome variation at the population level?
Low coverage whole genome sequencing, reduced-representation sequencing, and targeted enrichment
What is the main advantage of low/ultra-low coverage sequencing?
Data for the entire genome of multiple individuals and increased likelihood of detecting all alleles
What does whole genome sequencing involve?
Sequencing the entire genome
What should be considered for sequencing?
Capture amount, specificity, variability, reproducibility, cost, and input DNA
Study Notes
Advances in Genomic Sequencing Technologies and Strategies
- Assembly using short reads combined with large mate libraries at different coverages helps assemble larger contigs
- Comparisons between assembly programs should consider speed, error, number of contigs, and contig length
- Velvet is a highly efficient genome assembly program for short DNA sequence reads
- Genome re-sequencing aims to gather data on genetic variation through mapping reads to a known reference sequence
- Structural variation analysis leverages the distance and orientation between paired reads to provide insights on genome structure
- Bridge amplification is used in Illumina sequencing flow cells to amplify DNA fragments for sequencing
- N50 for a given genome assembly with contig lengths of 5mb, 25mb, 40mb, and 30mb is calculated as 30mb
- Large scaffolds in genomes with many repeats can be generated using mate pair libraries and methods that produce very long reads
- Whole genome sequencing involves sequencing the entire genome, while enrichment targets specific genomic regions
- Cost-saving approaches for genome variation at the population level include low coverage whole genome sequencing, reduced-representation sequencing, and targeted enrichment
- Considerations for sequencing include capture amount, specificity, variability, reproducibility, cost, and input DNA
- Advantages of low/ultra-low coverage sequencing include data for the entire genome of multiple individuals and increased likelihood of detecting all alleles
Test your knowledge about recent advances in genomic sequencing technologies and strategies with this quiz. Explore topics such as genome assembly, re-sequencing, structural variation analysis, sequencing platforms, and cost-saving approaches for population-level variation studies.
Make Your Own Quizzes and Flashcards
Convert your notes into interactive study material.
Get started for free
