Week 10 (Genome Assembly)

Question 1

all assembly relies on what simple assumption?

Answer 1

that highly similar DNA fragments originate from the same position within a genome

Question 2

all ______ approaches rely on the simple assumption that highly similar DNA fragments originate from the same position within a genome

Answer 2

assembly

Question 3

during genome assembly, it is important that highly similar DNA fragments originate from the same position within a genome. How does this apply to repetitive sequences in the genome? How do we resolve this?

Answer 3

repetitive sequences pose a challenge for genome assembly because they appear at multiple locations in the genome. we can resolve this by having longer sequences read so that they span the repeat or include the unique sequences around them.

Question 4

what are 3 critical properties of sequencing reads

Answer 4

1. length
2. accuracy
3. evenness

Question 5

comparatively to long read sequencing, ______ read genome sequencing is no longer relevant

Answer 5

short

Question 6

contig

Answer 6

set of sequence reads that overlap to form a contiguous stretch of DNA sequence

Question 7

a _______ is a set of sequence reads that overlap to form a contiguous stretch of DNA sequence

Answer 7

contig

Question 8

_______ numbers better = bigger contigs

Answer 8

lower

Question 9

N50

Answer 9

shortest contig length such that 50% of the bases contained in contigs of length N

Question 10

_____ is the shortest contig length such that 50% of the bases contained in contigs of length N

Answer 10

N50

Question 11

for N50, is higher or lower better?

Answer 11

higher

Question 12

L50

Answer 12

smaller number of contigs whose length sum to N50

Question 13

_____ is the smaller number of contigs whose length sum to N50

Answer 13

L50

Question 14

for L50, is higher or lower better?

Answer 14

lower

Question 15

De Bruin graph

Answer 15

assembly method that uses smaller sub-sequences (k-mers) of sequence reads to find overlaps and build a graph

Question 16

__________ ________ is an assembly method that uses smaller sub-sequences (k-mers) of sequence reads to find overlaps and build a graph

Answer 16

De Bruijn graph

Question 17

OLC assembly method

Answer 17

Overlap Layout Consensus

Question 18

what does each letter mean in OLC assembly method?

Answer 18

• Overlap: find all pairwise overlaps between all reads
• Layout: use those overlaps to determine how the reads should be put together
• Consensus: produce a consensus based on the layout and overlap of reads

.

Question 19

what does the O mean in OLC assembly method?

Answer 19

Overlap: find all pairwise overlaps between all reads

Question 20

what does the L mean in OLC assembly method?

Answer 20

Layout: use those overlaps to determine how the reads should be put together

Question 21

what does the C mean in OLC assembly method?

Answer 21

Consensus: produce a consensus based on the layout and overlap of reads

Question 22

T2T assembly recipe

Answer 22

1. error correction of accurate long reads
2. assembly graph construction
3. graph simplification with ultra long reads
4. phasing and scaffolding

Question 23

______ _______ to establish parent origin

Answer 23

k-mer counting

Question 24

what makes full siblings genetically different from each other?

Answer 24

crossing over / recombination during meiosis

Question 25

on average there is ___ million differences in DNA from person to person

Answer 25

3

Question 26

if we have the DNA of the parents, how can we distinguish what chromosomes came from mom and which from dad?

Answer 26

check for variance in the individual and compare it to the parents and establish parent of origin using k-mer counting

Question 27

bubble

Answer 27

polymorphisms between haplotypes

Question 28

a ______ is used to show polymorphisms between haplotypes

Answer 28

bubble

Question 29

tangle

Answer 29

region with complicated haplotypes not able to be resolved

Question 30

a ______ is a region with complicated haplotypes not able to be resolved

Answer 30

tangle

Question 31

which structural features must be present for a chromosome to be considered T2T?

Answer 31

centromere and telomeres on both ends

Question 32

BUSCO

Answer 32

benchmarking universal single-copy orthologs

Question 33

how is BUSCO made?

Answer 33

a way to evaluate how good we did at assembling the genome. There are 3023 genes in all vertebrates, so this method allows you to compare the 3000 genes with your genome to see how many you assembled and if they were assembled correctly

Question 34

What are our options for the types of reads to use for k-mer counting? Which do you think would produce the most accurate estimate of assembly base quality?

Answer 34

- raw reads, processed reads, error-corrects reads, short reads, long reads - For the most accurate estimate of assembly base quality, using long, error-corrected reads, ideally paired-end or mate-pair reads, is recommended.

Question 35

what is BUSCO used for?

Answer 35

a valuable tool for evaluating the completeness of an assembly

Question 36

it is now a common practice to use ______ to estimate the base accuracy of contig sequences, often measured in the Phred scale as quality value

Answer 36

kmers

Question 37

the count of kmers for heterozygous (30x coverage) is _____ of what the count for homozygous (60x coverage) is

Answer 37

half

Question 38

what are the three A's?

Answer 38

- assemblies - alignments - annotations

Question 39

describe the process that uses three A's

Answer 39

first you make a haploid genome ASSEMBLY, then ALIGN them to find variation, then you must ANNOTATE them (meaning that you need to find where the genes and regulatory elements are)

Question 40

on average there are a lower amount of sites for structural variants but is a _______ percentage in the diploid genome

Answer 40

higher

Question 41

pangenome

Answer 41

using multiple genomes and comparing them

Question 42

what term is used for a collection of genomes from multiple individuals of the same species that is a comprehensive representation of genetic diversity within a species?

Answer 42

pangenome

Question 43

what is the goal of a pangenome?

Answer 43

identify genetic variation within populations and individuals and associate them with something of interest

Question 44

what is this a visual representation of?

Answer 44

what a T2T genome assembly looks like, (red and blue represents mom and dads chromosome)

Question 45

what is an rDNA array? why do they exist? why are they hard to assemble?

Answer 45

ribosome is made of RNA and does translation, need a lot of ribosomes and lots of copied of ribosomal genes, need multiple loci for it to actually work (a lot of copies), put the copies right next to each other (tandem repeats), largely the same sequence on multiple chromosome

Question 46

rDNA ______: the last really hard part of a genome to assemble

Answer 46

tangle

Question 47

when does recombination occur?

Answer 47

during prophase 1 of meiosis

Question 48

what are tandem repeats?

Answer 48

DNA sequences where a short DNA motif (2-6 base pairs) is repeated consecutively along a chromosome, often found in non-coding regions, and can be used as genetic markers (often an area where there can be continuous generation)