GWAS

Question 1

long vs short k-mer tradeoff

Answer 1

long k-mers make a less tangled genome, short k-mers mean more of the genome can be assembled, as gaps will make less of a difference

Question 2

what improves N50?

Answer 2

longer starting depths
higher read depth
targeted sequencing of gaps post-assembly

Question 3

mate-paired reads

Answer 3

sequencing both ends of a genomic fragment, helps with assembly

Question 4

what is the point of genome-wide alignment

Answer 4

figuring out the function of genes
reconstructing their history
looking at selection
genomic signatures of convergent evolution

Question 5

examples of structural genomic changes

Answer 5

chromosomal inversions
gene duplication
gene loss
loss/gain of TEs

Question 6

heirarchical vs local WGA

Answer 6

heirarchical- quick ID of orthology across the genome, aligning ‘blocks’
local- producing nucleotide alignments, then filtering and merging sets to get orthologous segments

Question 7

dN/dS

Answer 7

measure of non-synonymous vs synonymous mutations
=1 under neutrality
less than 1 under purifying selection
over 1 under positive selection

Question 8

how can you test a hypothesis of convergent evolution?

Answer 8

look at where there are similarities between groups genomically, and track what those genes do- if you find links with the genome regions and the traits, it may have evolved convergently