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NGS > Alignment and denovo > Flashcards

Alignment and denovo Flashcards

1
Q

What does alignment in NGS refer to?

A

Matching DNA sequences to a reference genome

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2
Q

Which algorithm is commonly used in sequence alignment?

A

Needleman-Wunsch

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3
Q

What is the purpose of using a seed in alignment algorithms?

A

To initiate the alignment process efficiently

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4
Q

What is a ‘read’ in the context of NGS alignment?

A

A fragment of DNA sequenced in an NGS run

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5
Q

What challenge does repetitive DNA pose in alignment?

A

Can lead to more than one alignments

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6
Q

What does the term ‘coverage’ mean in NGS?

A

The number of times a base is sequenced

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7
Q

What is ‘mapping’ in NGS data analysis?

A

Aligning reads to a reference genome

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8
Q

What role does a reference genome play in alignment?

A

Provides a template to compare against sequenced reads

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9
Q

What is an advantage of paired-end sequencing in alignment?

repeted

A

Helps finding regoins that have been repeted

repeted

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10
Q

What does the Burrows-Wheeler Transform (BWT) do in sequence alignment?

A

Compresses DNA sequences

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11
Q

What is the significance of gap penalties in sequence alignment?

A

To penalize insertions and deletions

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12
Q

What is a primary challenge in aligning short reads in NGS?

A

They may align to multiple locations

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13
Q

What is the Smith-Waterman algorithm primarily used for?

A

Local sequence alignment

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14
Q

What does ‘consensus sequence’ mean in the context of alignment?

A

The most common sequence in a dataset

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15
Q

How does base quality scoring impact alignment?

A

Higher quality scores improve alignment accuracy

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15
Q

What is the role of ‘alignment score’ in NGS?

A

To assess the quality of the alignment

16
Q

Why are reference genomes updated periodically?

A

To correct errors and incorporate new genetic information

17
Q

What does ‘chimeric alignment’ refer to in NGS?

A

A single read aligning to two different parts of the genome

18
Q

What advantage does ‘splice-aware’ alignment offer for RNA-seq data?

A

It aligns reads across exon junctions

19
Q

In NGS, what is ‘indel realignment’ used for?

A

To correct mismatches in the alignment

20
Q

What is the primary goal of de novo assembly in NGS?

A

Assemble sequences without a reference genome

21
Q

What does “de novo” mean in the context of genome assembly?

A

From the beginning

22
Q

Which graph type is commonly used in de novo assembly?

A

De Brujin graph

23
Q

What are ‘contigs’ in de novo assembly?

A

Overlapping DNA sequences joined together

24
Q

What is the purpose of using k-mers in de novo assembly?

A

To break down reads into smaller parts for assembly

25
Q

What challenge do repeats in DNA pose for de novo assembly?

A

They make it difficult to accurately assemble sequences

26
Q

What is the role of mate-pair information in de novo assembly?

long range

A

To provide long-range continuity

27
Q

What does the term ‘coverage’ refer to in de novo assembly?

A

The depth of sequencing of a particular region

28
Q

Why is high coverage important in de novo assembly?

A

To ensure accuracy and completeness of the assembly

29
Q

What is a ‘scaffold’ in genome assembly?

A

A set of contigs ordered and oriented with gaps between them

30
Q

Which technology provides longer read lengths beneficial for de novo assembly?

A

Sanger sequencing

31
Q

How does the choice of k-mer size impact de novo assembly?

A

It affects the complexity and accuracy of the assembly

32
Q

What is a common problem in assembling highly repetitive DNA regions?

A

Uncertanity in placing repeats accurately

33
Q

In de novo assembly, what is the significance of ‘N50’?

A

It represents the length of the median contig

34
Q

What does the ‘greedy algorithm’ do in de novo assembly?

A

It merges fragments with the largest overlap first

35
Q

How do assemblers handle sequencing errors in de novo assembly?

A

They correct errors based on coverage and consensus

36
Q

Why is iterative k-mer analysis used in de novo assembly?

A

To find the optimal k-mer size for assembly

37
Q

What is the outcome of successful de novo assembly?

A

A complete and accurate representation of the sequenced genome

38
Q

How do paired-end reads aid in de novo assembly?

orientationand distance

A

By providing information about read orientation and distance

NGS (4 decks)

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