L6

Question 1

Fastq format

Answer 1

-A FASTQ file normally uses four lines per sequence.

Question 2

Line 1 of fastq format

Answer 2

begins with a ‘@’ character and is followed by a sequence identifier and an optional description.

Question 3

Line 2 of fastq format

Answer 3

raw sequence letters.

Question 4

Line 3 of the fastq format

Answer 4

begins with a ‘+’ character and is optionally followed by the same sequence identifier (and any description) again.

Question 5

Line 4 of the fastq format

Answer 5

encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.

Question 6

What do genome assembly programs do

Answer 6

stitch together an organism’s
chromosomes from fragmented reads of DNA

Question 7

Read

Answer 7

a DNA “word” that comes out of sequencer

Question 8

Contig

Answer 8

a contiguous sequence formed by several overlapping reads with no gaps that represent a consensus region of DNA

Question 9

Supercontig

Answer 9

an ordered and oriented set of contigs, usually by mate pairs

Question 10

N50

Answer 10

contig size of N means that 50% of the assembled bases are contained in
contigs of length N or larger.

Question 11

Coverage

Answer 11

The number of times a genome has been sequenced (the depth of
sequencing). C = LN / G

Question 12

Assembly size

Answer 12

Number of nucleotides successfully assembled

Question 13

A scaffold is made of

Answer 13

contigs and gaps

Question 14

How can gap length be guessed correctly

Answer 14

by incorporating information from paired ends or mate pairs of
different insert sizes

Question 15

Resequencing

Answer 15

• Allows us to investigate potential SNPs associated with
  disease.
• Allows us to investigate potential SNPs associated with
  individual populations.
• Allows us to investigate potential SNPs associated with
  niche specification.

Question 16

De novo sequence assembly

Answer 16

assembling reads together so that they form a new, previously unknown sequence. orders of magnitude slower and more memory intensive than mapping assemblers. No reference genome

Question 17

Comparative sequence assembly

Answer 17

assembling reads against and existing backbone or reference sequence, building a sequence that is similar but not necessarily identical to the backbone sequence.

Question 18

In absence of reference genome, what do we rely on

Answer 18

de novo assemblers

Question 19

What do de novo assemblers rely on

Answer 19

fact that 2 reads that overlap significantly in their sequence are likely to represent neighboring segments of a
genome. (Kmer value)

Question 20

When do problems arise with de novo assemblers

Answer 20

when overlapping regions belong to
repetitive regions.

Question 21

What is the popular sequencing choice for De novo assembly

Answer 21

PacBio sequencing due to low costs

Question 22

Greedy assembly algorithm

Answer 22

It is used for organisms such as bacteria, single-celled eukaryotes as they have single genomes and aren’t repetitive. It has some efficiency limitation.

Question 23

What has the greedy algorithm been superseded by

Answer 23

Graph methods

Question 24

Steps of greedy algorithm

Answer 24

Calculate pairwise alignments of all fragments.
(2) Choose two fragments with the largest overlap.
(3) Merge chosen fragments.
(4) Repeat step 2 and 3 until only one fragment is left.

Question 25

Alternative to greedy algorithm

Answer 25

de Brujin graphs- ask if its eulerian

Question 26

What is an eulerian graph

Answer 26

A graph is considered Eulerian if the graph is both connected and has a closed trail (a walk with no repeated edges)
containing all edges of the graph.

Question 27

What does it mean when a graph is connected

Answer 27

if each node can be reached by some other
node.
* Node is balanced if indegree equals outdegree.
* Node is semi-balanced if indegree differs from outdegree by 1.
* A directed, connected graph is Eulerian if and only if it has at most
2 semi-balanced nodes and all other nodes are balanced.