Sequencing and Quality Control

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What is the primary purpose of De-novo assembly in NGS?

To annotate bacterial and archaeal genomes

To detect SNPs and structural variations (correct)

To identify the genome size

To assess the quality of assembled data

What determines the number of times sequenced nucleotide bases cover the target genome?

Genome size

Sequencing depth (correct)

Contig length

Sequencing coverage

What is the definition of N50 score?

The number of contigs in the assembly

The sequence length of the shortest contig at 50% of the assembly length (correct)

The longest contig in the assembly

The total length of all contigs

What is the purpose of RAST annotation?

To annotate bacterial and archaeal genomes Signup and view all the answers

What is the minimum sequencing coverage required for De-novo assembly?

30-50 X Signup and view all the answers

What is the purpose of FastQC?

To provide an overview of basic quality control metrics for raw next-generation sequencing data Signup and view all the answers

What is the purpose of sequence assembly?

To merge short DNA sequence fragments into a longer DNA sequence Signup and view all the answers

What is the term for the smallest number of contigs whose length sum makes up half of the assembly size?

L50 count Signup and view all the answers

What is a characteristic of re-sequencing assembly?

It requires a good reference genome Signup and view all the answers

What is the relationship between Phred Quality Scores (Q scores) and base calling error probabilities (P)?

Q scores are logarithmically related to P Signup and view all the answers

What is the advantage of re-sequencing assembly over de novo assembly?

It is easier and more rapid Signup and view all the answers

What is the name of a commonly used tool for sequence assembly?

SPAdes Signup and view all the answers

What was the first fully sequenced amino acid sequence in 1953?

Bovine insulin Signup and view all the answers

What is a limitation of the chain-termination method in DNA sequencing?

It can only be used for short DNA sequences less than 1000 bp Signup and view all the answers

What is the purpose of shotgun sequencing?

To sequence entire chromosomes Signup and view all the answers

What is the difference between clone-by-clone and whole-genome shotgun sequencing?

Clone-by-clone involves mapping and cloning before sequencing, while whole-genome shotgun does not Signup and view all the answers

What is the first step in DNA sequencing?

DNA extraction Signup and view all the answers

What is the advantage of whole-genome sequencing?

It allows for the detection of sequence variations, genome-wide association analysis, and non-conventional breeding Signup and view all the answers