Assembly Lecture Flashcards

1
Q

All assembly approaches rely on the simple assumption that

A

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

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2
Q

What has a fundamental impact on the complexity of assembly

A

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

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3
Q

Contig

A

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

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4
Q

N50

A

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

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5
Q

L50

A

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

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6
Q

De Bruijn graph

A

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

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7
Q

OLC-overlap layout consensus

A

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

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8
Q

BUSCO

A

benchmarking universal single-copy orthologs

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9
Q

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

A

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

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