Assembly Lecture

Question 1

All assembly approaches rely on the simple assumption that

Answer 1

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

Question 2

What has a fundamental impact on the complexity of assembly

Answer 2

read length
longer reads have more unique DNA-easier to assembly

Question 3

Contig

Answer 3

set of sequence reads that overlap to form a contigous stretch of DNA sequence
Lower numbers are better= bigger contigs

Question 4

N50

Answer 4

shortest contig length such that 50% of the bases are contained in contigs of length N (higher is better)

Question 5

L50

Answer 5

smallest number of contigs whose length sum to N50 (lower is better)

Question 6

De Bruijn graph

Answer 6

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

Question 7

OLC-overlap layout consensus

Answer 7

assembly method
-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 8

BUSCO

Answer 8

benchmarking universal single-copy orthologs

Question 9

To better capture the variation missed by using one reference, we can create and utilize a

Answer 9

pan-genome
a collection of al the DNA sequences that occur in a species